Biocview "Software"

Access Bioconductor docker images
Access Bioconductor docker images
Access Bioconductor docker images
Access HDF5 content from h5serv
Access HDF5 content from h5serv
Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
Accurate Inference of Genetic Ancestry from Cancer Sequencing
Accurate Inference of Genetic Ancestry from Cancer Sequencing
A collection of single-cell V(D)J tools
A collection of single-cell V(D)J tools
A collection of tools for imaging MS data processing
A collection of tools for imaging MS data processing
A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions
A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions
A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions
A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
Adaptive Signature Selection and InteGratioN (ASSIGN)
Adaptive Signature Selection and InteGratioN (ASSIGN)
Adaptive Signature Selection and InteGratioN (ASSIGN)
Advanced analysis of microbial flow cytometry data
A fast hierarchical graph-based clustering method
A Fast Scalable and Flexible Non Negative Matrix Factorization Method
Affinity test for identifying regularity Indels
Affinity test for identifying regulatory SNPs
Affinity test for identifying regulatory SNPs
Affymetrix-based RMA Processing Using Fixed Parameters
A Framework for Consensus Partitioning
A Framework for Consensus Partitioning
A Framework for Quality Control
A Framework for Quality Control
A Framework for visualizing gene set enrichment throughout neurodevelopment
A Framework for visualizing gene set enrichment throughout neurodevelopment
A Framework to Combine, Analize and Interpret CNVs Calling Results
A gene-signature ranking method based on sample density in PCA space
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
A graphical user interface for MSstatsQC package
A graphical user interface for MSstatsQC package
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
Allele-specific copy number genotyping for single cell sequencing data
A mass spectrometry imaging toolbox for statistical analysis
An algorithm for gene and gene set network inference
An alternative to dendrogram visualization and insertion of multiple layers of information
An alternative to dendrogram visualization and insertion of multiple layers of information
Analysis of alternative poly A site usage
Analysis of Brain Imaging Data
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Analysis of compositions of microbiomes with bias correction
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analysis of FACS data for the Jurkat crible project
Analysis of high-throughput microscopy-based screens
Analysis of Large-Scale Pharmacogenomic Data
Analysis of Large-Scale Pharmacogenomic Data
Analysis of Large-Scale Radio-Genomic Data
Analysis of Large-Scale Radio-Genomic Data
Analysis of Large-Scale Toxico-Genomic Data
Analysis of Large-Scale Toxico-Genomic Data
Analysis of patient-derived xenograft (PDX) data
Analysis of patient-derived xenograft (PDX) data
Analysis of pooled genetic screens
Analysis of pooled genetic screens
Analysis of single-cell epigenomics datasets with a Shiny App
Analysis of single-cell epigenomics datasets with a Shiny App
Analysis of Transposable Elements
Analysis Tools for 10X V(D)J Data
Analysis Tools for scATACseq Data with CoGAPS
Analyze comorbidities from electronic health record data
Analyze flow cytometric data using gate information
Analyze flow cytometric data using histogram information
Analyze Gene Sets Collections Properites
Analyze high-throughput sequencing of T and B cell receptors
Analyze high-throughput sequencing of T and B cell receptors
Analyze high-throughput sequencing of T and B cell receptors
Analyze massively parallel reporter assays
Analyze massively parallel reporter assays
Analyze the Neighborhood (Upstream/Downstream Neighbors) of Genes
Analyzing tRNA sequences and structures
Analyzing tRNA sequences and structures
An Easy Pipeline for NanoString nCounter Data Analysis
An Implementation of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection
An integrated analysis package of Gene expression and Copy number alteration
An integrated analysis package of miRNA and mRNA expression data
An integrated analysis package of miRNA and mRNA expression data
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
An interface to the Semantic MEDLINE database
An interface to the Semantic MEDLINE database
annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions
Annotate sequences with KEGG pathways
Annotate the Gene Symbols for Probes in Expression Array
Annotate transcripts and predicted protein sequences
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Annotation and gene expression data retrieval from Bgee database
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
Annotation of Genomic Regions to Genomic Annotations
Annotation of Genomic Regions to Genomic Annotations
annotation of noncoding RNAs and coexpressed genes
annotation of noncoding RNAs and coexpressed genes
Annotation translation functions
ANother Transcriptome Lineage ExploreR
a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
An package for identification of novel peptides by customized database derived from RNA-Seq
An package for identification of novel peptides by customized database derived from RNA-Seq
An package for identification of novel peptides by customized database derived from RNA-Seq
An R Interface for Ribo Files
An R Interface for Ribo Files
An R Interface for Ribo Files
An R interface to the Common Workflow Language
An R interface to the Common Workflow Language
An R interface to the Common Workflow Language
An R interface to the Ontology Lookup Service
An R interface to the Ontology Lookup Service
An R Package for Adjusting Bias in Gene Set Enrichment Analysis
an R package for analysis, visualization and biomarker discovery of microbiome
An R package for circadian and differential circadian analysis.
An R package for circadian and differential circadian analysis with repeated measurement
An R package for circadian differential R2.
An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
An R package for DiffCircaPipeline: A framework for multifaceted characterization of differential rhythmicity
An R package for fast computing for adaptively weighted fisher's method
An R package for fast computing for adaptively weighted fisher's method
An R Package for Integrating and Visualizing Single-Cell and Bulk Data to Resolve Regulatory Elements
An R package for subset-based association analysis of heterogeneous traits and subtypes
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for the creation of complex genomic profile plots
An R package for the creation of complex genomic profile plots
An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms
An R Package for Unbiased Splicing Pathway Analysis
An R Package for Unbiased Splicing Pathway Analysis in RNAseq data
an R package for visualization of tree and annotation data
an R package for visualization of tree and annotation data
an R package for visualization of tree and annotation data
An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
An R package to automate the analysis of double-strand break repair during meiosis
An R package to simulate DNA methylation data
An R/shiny package for microbiome functional enrichment analysis
An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).
AnVILBilling
A package for visualizing complex biological network
A package of creating an algorithm of identifying microRNA-competing endogenous RNA triplets
A package to search and retrieve data from Hub resources
A package with style requirements for the gDR suite
A pipeline for processing drug sensitivity screen data
A Pipeline Manager
A Pipeline to Process RNAseq Data
A Pipeline to Process RNAseq Data
Application of t-sne to NGS Genomic Signal Profiles
A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data
A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data
A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data
ArrayAnalysis
ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression
A search tool for single cell RNA-seq data by gene lists
A search tool for single cell RNA-seq data by gene lists
A sensitive and fast tool for detection of TAD boundaries
A set of methods and tools for comprehensive analysis of phosphoproteomics data
A set of methods and tools for comprehensive analysis of phosphoproteomics data
A set of methods and tools for comprehensive analysis of phosphoproteomics data
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
A Shiny App to accompany clusterExperiment
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
Assigning scRNA-seq to clone-of-origin using copy number from ultra-low-depth scDNA-seq
Assign Properties to TNBC Patients
Assign Properties to TNBC Patients
Assign rfPred functional prediction scores to a missense variants list
Associates DNA Methylation with Matched gene Expression
Associates DNA Methylation with Matched gene Expression
Associates DNA Methylation with Matched gene Expression
A suite of functions to facilitate zFPKM transformations
A suite of functions to facilitate zFPKM transformations
A SummarizedExperiment for Ivy-GAP data
A SummarizedExperiment for Ivy-GAP data
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data
Asymmetric Within-Sample Transformation
Atlas and Analysis of Systems-Biology-Led Pathways
A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)
A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)
A tool for unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
A toolkit for APA analysis using RNA-seq data
A toolkit for APA analysis using RNA-seq data
A Toolkit for Flow And Mass Cytometry Data
A Toolkit for Flow And Mass Cytometry Data
A Toolkit for Flow And Mass Cytometry Data
A Toolkit for Flow And Mass Cytometry Data
A toolkit for performing KNN-based statistics for flow and mass cytometry data
A toolkit for performing KNN-based statistics for flow and mass cytometry data
A toolkit for single-cell immune receptor profiling
A toolkit for single-cell immune receptor profiling
A tool set for 3D Trans-Omic network visualization with Cytoscape
A tool set for 3D Trans-Omic network visualization with Cytoscape
A tool to calculate and validate primers for Golden Gate Cloning
Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions
Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Automated functions for comparing various omic data from cbioportal.org
Automated functions for comparing various omic data from cbioportal.org
Automated functions for comparing various omic data from cbioportal.org
Automated ingestion and conversion of various single-cell data formats.
Automated, probabilistic assignment of scRNA-seq to cell types
Automated Seurat Pipeline for scRNA-seq analysis
Automated spectraL Processing System for NMR
Automated spectraL Processing System for NMR
Automate package and project setup for Bioconductor packages
Automate package and project setup for Bioconductor packages
Automatically Aggregating and Summarizing lncRNA Analysis Results for Interactive Report
Automatically Aggregating and Summarizing lncRNA Analysis Results for Interactive Report
Automatic RNA-Seq present/absent gene expression calls generation
Automatic RNA-Seq present/absent gene expression calls generation
Automatic Statistical Identification in Complex Spectra
Automatic Statistical Identification in Complex Spectra
A visualization tool for single cell data of C.elegans embrogenesis
A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses
A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses
A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses
A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
Bandwise normalization and batch correction of Hi-C data
Bandwise normalization and batch correction of Hi-C data
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes for Storing Genomic Interaction Data
Base Classes for Storing Genomic Interaction Data
BASiNET - Classification of mRNA and lncRNA sequences using complex network theory
Batch Effects Quality Control Software
Batch Effects Quality Control Software
Bayesian ANalysis Of Compositional Covariance
Bayesian ANalysis Of Compositional Covariance
Bayesian ANalysis Of Compositional Covariance
Bayesian Analysis of Differential Expression in RNA Sequencing Data
Bayesian Analysis of Single-Cell Sequencing data
Bayesian Analysis of Single-Cell Sequencing data
Bayesian Enrichment Estimation in R
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Bayesian hierarchical model for genome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)
bcbioLite
BEAT - BS-Seq Epimutation Analysis Toolkit
Benchmark of differential abundance methods on microbiome data
Bias-free Footprint Enrichment Test
Bias-free Footprint Enrichment Test
Big multivariate data plotted interactively
Binomial Random Forest Feature Selection
Binomial Random Forest Feature Selection
Bioconductor Quality Enhancement
Bioconductor software ecosystem building tools
biodb, a library and a development framework for connecting to chemical and biological databases
biodbChebi, a library for connecting to the ChEBI Database
biodbExpasy, a library for connecting to Expasy ENZYME database.
biodbHmdb, a library for connecting to the HMDB Database
biodbKegg, a library for connecting to the KEGG Database
biodbLipidmaps, a library for connecting to the Lipidmaps Structure database
biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database
biodbUniprot, a library for connecting to the Uniprot Database
Biogeographic Regionalization and Macroecology
Biogeographic Regionalization and Macroecology
Bioinformatics pipelines based on Rcwl
Bioinformatics pipelines based on Rcwl
Bioinformatics pipelines based on Rcwl
Biological Network Reconstruction Omnibus
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
BioTIP: An R package for characterization of Biological Tipping-Point
BioTIP: An R package for characterization of Biological Tipping-Point
BioTIP: An R package for characterization of Biological Tipping-Point
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
Build Annotation From Online Database
Bumpy Matrix of Non-Scalar Objects
Cache files downloaded from S3
Calculate and Visualize Synergy Scores for Drug Combinations
Calculate and Visualize Synergy Scores for Drug Combinations
Calculate and Visualize Synergy Scores for Drug Combinations
Calculate and Visualize Synergy Scores for Drug Combinations
Calculate and Visualize Synergy Scores for Drug Combinations
Calculate growth-rate inhibition (GR) metrics
Calculate growth-rate inhibition (GR) metrics
Calculate growth-rate inhibition (GR) metrics
Calculate, visualize and analyse overlap between genomic regions
Calling CMS for mouse tissue
Cancer mutation analysis
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Candidate Driver Analysis
Candidate Driver Analysis
Candidate Gene Miner
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Casc
ccrepe_and_nc.score
ccrepe_and_nc.score
cell counter
Cell-Cycle using Mixture Models
Cell type annotation for unannotated single-cell RNA-Seq data
Cell type annotation for unannotated single-cell RNA-Seq data
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
Cepo for the identification of differentially stable genes
Challenges for the Bioconductor community
Challenges for the Bioconductor community
Check Multiple Covariates for Potenial Confounding Effects
Check Yeast Deletion Barcodes
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.
Chromosome Instability Index
Chromosome Instability Index
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
Classes and Functions to Serve as the Basis for Other 'Gx' Packages
Classes and Functions to Serve as the Basis for Other 'Gx' Packages
Classes and Functions to Serve as the Basis for Other 'Gx' Packages
Classes and Methods for Handling Genomic Interaction Data
Classes and methods for multi-omics data integration
Classes and methods for multi-omics data integration
Classes and methods for multi-omics data integration
Classes and methods for performing benchmark comparisons
Classes and methods for performing benchmark comparisons
Classification of RNA-seq data from ALL samples
Classification of RNA Sequences using Complex Network and Information Theory
Classification of RNA Sequences using Complex Network Theory
Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
Client for GREAT Analysis
Client for GREAT Analysis
Clonal ordering and visualization
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations
Clone Identification from Single Cell Data
Clone Identification from Single Cell Data
Clone Identification from Single Cell Data
Cluster analysis of Spatial Transcriptomics data
Cluster analysis of Spatial Transcriptomics data
Clustering Algorithms for Bioconductor
Clustering Algorithms for Bioconductor
Clustering and pathway analysis using exponential distributions
Clustering and Resolution Enhancement of Spatial Transcriptomes
Clustering and Resolution Enhancement of Spatial Transcriptomes
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering approach to solve complete Deconvolution problem
Clustering Deviation Index (CDI)
Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq
CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile
CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models
CNCDriver
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
Code for using BridgeDb identifier mapping framework from within R
Code for using BridgeDb identifier mapping framework from within R
Codon Usage Analysis and Prediction of Gene Expressivity
Codon Usage Analysis and Prediction of Gene Expressivity
Co-Expression Analysis of Sequencing Data
Co-Expression Analysis of Sequencing Data
Co-Expression Analysis of Sequencing Data
co-expression of lincRNAs and protein-coding genes
co-expression of lincRNAs and protein-coding genes
Collate Gene Annotation Data from Uniprot and NIH Gene Databases
Collection of simple tools for learning about Bioconductor Packages
Collection of simple tools for learning about Bioc Packages
Collection of simple tools for learning about Bioc Packages
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
Common utility functions
Comparative Evaluation and Visualization of Differential Expression Analyses
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets
Compare Patient Samples to Cell Line Models Using Molecular Data and Weighted Similarity
Compares the genetic/epigenetic features between cancer cell lines with different dependencies of a gene set (signature)
Comparing tumour copy number profiles
Compensates for the bias introduced by median normalization in phosphoproteomics. This is done by taking enriched and non-enriched data and creating a normalization factor.
Competitive Balances for Taxonomic Enrichment Analysis in R
Competitive Balances for Taxonomic Enrichment Analysis in R
CompositeDriver
Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Compute coverage matrices from recount quickly using bwtool
Conditional Differential Analysis for Flow and Mass Cytometry Experiments
Conditional reciprocal best hits (CRBHits) in R
Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation
Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation
Confidence estimation for intra-chromosomal contact maps
Confidence estimation for intra-chromosomal contact maps
Confidence estimation for intra-chromosomal contact maps
Confidence estimation for intra-chromosomal contact maps
ConsensusClusterPlus
ConsensusClusterPlus
Construct Benchmarks for Single Cell Analysis Methods
Construct Benchmarks for Single Cell Analysis Methods
Constructing gene regulatory networks from expression data through functional module inference
Constructing gene regulatory networks from expression data through functional module inference
Constructing gene regulatory networks from expression data through functional module inference
Context-Aware Transcript Quantification from Long Read RNA-Seq data
Conversion of single cell experiment output files to relational database
Convex Analysis of Mixtures for Tissue Heterogeneity Characterization
Convex Analysis of Mixtures for Tissue Heterogeneity Characterization
Convex Analysis of Mixtures Version 3
CopyKit
Copy Number Analysis for 450k Illumina Methylation Arrays
Copy number calling and SNV classification using targeted short read sequencing
Copy number calling and SNV classification using targeted short read sequencing
Copy Number Variant Metrics
Copy Number Variant Metrics
Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments
Correction of batch effects in DNA methylation data
Correction of batch effects in DNA methylation data
Correction of batch effects in DNA methylation data
Correlation analysis of RNA secondary structure mutation and differential expression
Correlation analysis of RNA secondary structure mutation and differential expression
Correspondence Analysis for Single Cell Data
Correspondence Analysis for Single Cell Data
Coverage visualization package for R
Create R package
Creates and uses physio spaces as a dimension reduction mapping
Creates diffusion maps
Creates diffusion maps
Creates hatched patterns for scatterplots
Creating a DelayedMatrix of Regression Residuals
Creating a DelayedMatrix of Regression Residuals
crisprseekplus
crisprseekplus
Crossover analysis and genetic map construction
CUE: CpG impUtation Ensemble for DNA Methylation Levels Across the HumanMethylation450 (HM450) BeadChip and HumanMethylation EPIC (HM850) BeadChip Platforms
Customize and Query Compound Annotation Database
Customize and Query Compound Annotation Database
Cutsomize and Query Compound Annotation Database
Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Data-driven Annotation of the Transcriptome
Data Package for the annoFuse Bioconductor Package
DataSHIELD client site Omics association functions.
DataSHIELD server site Omic functions
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Decomposition of individual tumors into mutational signatures by signature refitting
Decomposition of individual tumors into mutational signatures by signature refitting
Deconvolution by Convex Analysis of Mixtures
Deconvolution by Convex Analysis of Mixtures
Deconvolution of Expression for Nascent RNA Sequencing Data
Deconvolution of Expression for Nascent RNA Sequencing Data
decoupleR: Ensemble of computational methods to infer biological activities from omics data
DegNorm: degradation normalization for RNA-seq data
DegNorm: degradation normalization for RNA-seq data
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction
derfinder helper package
derfinder helper package
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions
detect different methylation level (DMR)
Detecting abberant splicing events from RNA-sequencing data
Detecting abberant splicing events from RNA-sequencing data
Detecting patterns of post-transcriptional modifications using machine learning
Detecting patterns of post-transcriptional modifications using machine learning
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Detection, Characterization and Visualization of Kataegis in Sequencing Data
Detection of 2'-O methylations by RiboMethSeq
Detection of 2'-O methylations by RiboMethSeq
Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
Detection of DE genes in time series data using impulse models
Detection of DE genes in time series data using impulse models
Detection of Differentially Methylated Regions
Detection of Differentially Methylated Regions
Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)
Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)
Detection of m7G, m3C and D modification by AlkAnilineSeq
Detection of m7G, m3C and D modification by AlkAnilineSeq
Detection of post-transcriptional modifications in high throughput sequencing data
Detection of post-transcriptional modifications in high throughput sequencing data
Detection of site fixation in molecular evolution
Detect marker panel from scRNA-seq profile
Detect marker panel from scRNA-seq profile
Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output
Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output
Determination of essential phenotypic elements of clusters in high-dimensional entities
Determination of essential phenotypic elements of clusters in high-dimensional entities
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Diagnostic Plots to Evaluate the Target Decoy Approach
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Differential abundance analysis with a right censored covariate in high-dimensional cytometry
Differential Alternative Polyadenylation Analysis From Compositions
Differential discovery in high-dimensional cytometry via high-resolution clustering
Differential discovery in high-dimensional cytometry via high-resolution clustering
Differential Enrichment Scan
Differential Enrichment Scan 2
Differential Enrichment Scan 2
Differential Epigenetic Coregulation Test
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups
Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups
Differential expression analysis of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Differential expression using kernel-based score test
Differential Gene Expression Analysis for Multi-subject scRNA-seq
Differential Gene Expression Analysis for Multi-subject scRNA-seq
Differentially Methylated Regions caller
Differentially Methylated Regions caller
Differentially regulated genes from scRNA-seq data
Differential neighbourhood abundance testing on a graph
Differential neighbourhood abundance testing on a graph
Differential pattern analysis for Ribo-seq data
Differential pattern analysis for Ribo-seq data
Differential RhythmicitY analysis
Differential Topology, Progression and Differentiation
Different methods for the integrative analysis multiple omics data
Different test statistics based on co-citation.
Different test statistics based on co-citation.
DiffLogo: A comparative visualisation of biooligomer motifs
DiffLogo: A comparative visualisation of biooligomer motifs
Direct Access to Orbitrap Data and Beyond
Direct Access to Orbitrap Data and Beyond
Discriminant Analysis for Evolutionary Inference
Discriminant Analysis for Evolutionary Inference
Disease-Gene-Variant Relations Mining from the Public Databases and Literature
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Displaying binary trees with focus on dendrogram leaves
distinct: a method for differential analyses via hierarchical permutation tests
Divergence Computations
Divergence: Functionality for assessing omics data by divergence with respect to a baseline
Divergence: Functionality for assessing omics data by divergence with respect to a baseline
Do 16s Data Analysis and Generate Figures
Do 16s Data Analysis and Generate Figures
doseLM
doseR
doseR
doseR
doseR
doseR
doseR
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
DtracePLN: Sparse precision matrix estimation via lasso penalized D-trace loss in the multivariate Poisson log-normal model
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
EaCoN : Easy Copy Number !
Earth Mover's Distance for Differential Analysis of Genomics Data
Earth Mover's Distance for Differential Analysis of Genomics Data
Easy Analysis of RNASeq DE
Easy Analysis of RNASeq DE
Easy single cell analysis platform for enrichment
Easy single cell analysis platform for enrichment
echoverse module: echoversePackageTitle
EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices
EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices
Ejemplo de biocthis para cdsb2020
Ejemplo de biocthis para ConectaR2021
ELBOW - Evaluating foLd change By the lOgit Way
Empirical Bayes estimate of block diagonal covariance matrices
Empirical Bayes estimate of block diagonal covariance matrices
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Enrichment Approach to Predict Which Transcription Factors are Regulated
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
EpiMethEx Package
EpiMix: an integrative tool for the population-level analysis of DNA methylation
Epistasis Analysis for Quantitative Traits by Functional Regression Model
Equality of 2 (or k) Continuous Univariate and Multivariate Distributions
Equality of 2 (or k) Continuous Univariate and Multivariate Distributions
Eric Utilities
Estimates Isoform Specific RPF Footprint Densities
Estimate Systems Immune Response from RNA-seq data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
EWCE for Multiple Gene Lists
ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
Exon Based Strategy for Expression Analysis of genes
Exploration of marker-gene sequence taxonomic annotations
Exploration of marker-gene sequence taxonomic annotations
Exploratory Data Analysis of LC-MS/MS data by spectral counts
Exploratory Systems Analysis Tools
Explore and download data from the recount3 project
Explore and download data from the recount3 project
Explore and download data from the recount project
Explore and download data from the recount project
Exploring the Human Cell Atlas Data Coordinating Platform
Exposes and makes available data from the cBioPortal web resources
Exposes and Makes Available Data from the cBioPortal Web Resources
Exposes and Makes Available Data from the cBioPortal Web Resources
Exposome exploration and outcome data analysis
Exposome exploration and outcome data analysis
Extending guilt by association by degree
Extending guilt by association by degree
Extra Base Functions for Bioconductor
Extract and manage matrix data from the Human Cell Atlas project
Extract and manage matrix data from the Human Cell Atlas project
Facilities for Filtering Bioconductor Annotation Resources
Facilities for Filtering Bioconductor Annotation Resources
Facilities for Filtering Bioconductor Annotation Resources
Facilities for Filtering Bioconductor Annotation Resources
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Factor Loading Adaptive SHrinkage in R
Fast and Interpretable Consensus Clustering via Minipatch Learning
Fast calculation of uniConSig and CSEA
Fast Permutation-based Gene Set Analysis
Fast Permutation-based Gene Set Analysis
FASTQ Quality Control
FASTQ Quality Control
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens
FDR-controlled analysis of 2D-TPP experiments with replicates
FDR-controlled analysis of SPP experiments
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Feature Specific Quantile Normalization
FEVV: Functional Enrichment of Genomic Variants and Variations
Find breakpoints in Strand-seq data
Find breakpoints in Strand-seq data
Find breakpoints in Strand-seq data
Find common transcription factors in yeast expression data
find influential TF and Target based on multi-omics data
Finding Mutually Exclusive Groups of Alterations in Cancer Datasets
Find microbial interactions
Find Potential Disease-Related Genes
Find RAre Splicing Events in RNA-Seq Data
Find RAre Splicing Events in RNA-Seq Data
Find RAre Splicing Events in RNA-Seq Data
Find SNV/Indel differences between two bam files with near relationship
FIREcaller: an R package for detecting frequently interacting regions from Hi-C data
Fit a Gamma-Poisson Generalized Linear Model
Fit a Gamma-Poisson Generalized Linear Model
Fix gene symbols that are messed up by Excel
flexible pipelines for secretome prediction
For Visualizing Differential Expression Analysis
Framework for Storing and Accessing Hi-C Data Through HDF Files
Framework for Storing and Accessing Hi-C Data Through HDF Files
Framework for Storing and Accessing Hi-C Data Through HDF Files
Framework for Storing and Accessing Hi-C Data Through HDF Files
From functional enrichment results to biological networks
Frozen RMA and Barcode
Frozen RMA and Barcode
Frozen RMA Tools
Frozen RMA Tools
Functional interpretation of single cell RNA-seq latent manifolds
Functional interpretation of single cell RNA-seq latent manifolds
Functionality Visualization for Motifs
Functions for Analyzing Cellular Barcoding Data
Functions for Analyzing Cellular Barcoding Data
Functions for analyzing SELEX-seq data
Functions for annotating GRanges objects
Functions for annotating GRanges objects
functions for genome-wide application of Liquid Association
functions for genome-wide application of Liquid Association
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
Functions to help analyze data as phyloseq objects
Functions to help analyze data as phyloseq objects
Functions used to preprocess datasets stored in BioDataome
Further Utilities for Genomic Interactions
GC-SIM-MS data processing and alaysis tool
GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens
GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens
Genearting Samples of Gene Expression Data with Variational Autoencoders
General utility functions for developing Bioconductor packages
General utility functions for developing Bioconductor packages
General utility functions for developing Bioconductor packages
General utility functions for developing Bioconductor packages
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Generate customized protein databases from NGS data for proteomics search
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate Publication Ready Visualizations of Single Cell Transcriptomics Data
Generate Publication Ready Visualizations of Single Cell Transcriptomics Data
Generate Quality Surrogate Variable Analysis for Degradation Correction
Generate Summary Plots of FastQC Reports
Generate synthetic nucleosome maps
Generate synthetic nucleosome maps
Generating Protein Sequences with Deep Generative Models
Generating SAM file for PSMs in shotgun proteomics data
Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions
Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Generation of cell pictures
Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
Generic Omics Pathway Enrichment Analysis
Gene set analysis accounting for gene-gene correlations
Gene set analysis following differential expression using linear (mixed) modeling with dream
Gene Set Analysis in R
Gene Set Enrichment Analysis with Networks
Gene Set Enrichment Analysis with Networks
Gene Set Enrichment / Projection Displays
Gene Set Enrichment / Projection Displays
Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
Genome Level Trellis Layout
Genome Level Trellis Layout
Genome Level Trellis Layout
GenoMetric Query Language for R/Bioconductor
GenoMetric Query Language for R/Bioconductor
Genome-wide assessment of differential translations with ribosome profiling data
Genome-wide assessment of differential translations with ribosome profiling data
Genomic Annotation in Livestock for Positional Candidate LOci
Genomic Annotation in Livestock for Positional Candidate LOci
GenomicDistributions: fast analysis of genomic intervals with Bioconductor
Genomic Knowledge-guided Multiple Testing
GenomicOperations
GenomicOperations
GEOexplorer: a webserver for gene expression analysis and visualisation
GEOexplorer: a webserver for gene expression analysis and visualisation
GEOexplorer: a webserver for gene expression analysis and visualisation
GEOsearch
GEOsearch
Get the QTL/gene/SNP data functions
gin in R
gin in R
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
GO-terms Semantic Similarity Measures
GO-terms Semantic Similarity Measures
GO-terms Semantic Similarity Measures
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
Graphical User Interface for High Performance BAM-based binary alternative splicing event quantitation, differential analysis, and visualisation
Graphical User Interface for IsoCorrectoR
Graphical User Interface for IsoCorrectoR
GREAT Analysis - Functional Enrichment on Genomic Regions
GRO-seq Analysis Pipeline
GRO-seq Analysis Pipeline
GRO-seq Analysis Pipeline
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
GWAS Incorporating Networks
GWAS Incorporating Networks
Handling Missing Individuals in Multi-Omics Data Integration
Handling Missing Individuals in Multi-Omics Data Integration
Handling Missing Individuals in Multi-Omics Data Integration
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
Helper Functions for LIBD Deconvolution
Helper Functions for LIBD Deconvolution
Hexbin plots for single cell omics data
Hexbin plots for single cell omics data
HiC analysis using data.table
HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
HiCdiff: Joint normalization and comparative analysis of multiple Hi-C datasets
Hi-C Direct Caller Plus
Hierarchical ensemble method based on factor graph
High-throughput prediction of DNA shape features
High-throughput prediction of DNA shape features
HLA typing clustering and visualization based on specific similarity metrics
HLA typing clustering and visualization based on specific similarity metrics
HMMERutils
HMMERutils
Human genome partitioning of dense sequencing data by identifying haplotype blocks
Human genome partitioning of dense sequencing data by identifying haplotype blocks
Identification and Analysis of ceRNA Regulation
Identification and analysis of miRNA sponge interaction networks and modules
Identification and analysis of miRNA sponge interaction networks and modules
Identification and analysis of miRNA sponge regulation
Identification and analysis of miRNA sponge regulation
Identification and Annotation of Protein Hotspot Residues
Identification and Annotation of Protein Hotspot Residues
Identification and classification of plant transcription factors
Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning
Identification of genetic Variants affecting Alternative Splicing
Identifying differential cell populations in flow cytometry data accounting for marker frequency
igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
Immunoglobulin Clonal Lineage and Diversity Analysis
Implementation of MultiDataSet and ResultSet
Implementation of MultiDataSet and ResultSet
Implementation of the dot bracket annotations with Biostrings
Implementation of the dot bracket annotations with Biostrings
Implements the Affymetrix PLIER algorithm
Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
Importing a tRNAscan-SE result file as GRanges object
Importing a tRNAscan-SE result file as GRanges object
Importing a tRNAscan-SE result file as GRanges object
Importing from tRNAdb and mitotRNAdb as GRanges objects
Importing from tRNAdb and mitotRNAdb as GRanges objects
Import methods for 10X Genomics files
Improving replicability in single-cell RNA-Seq cell type discovery
Improving replicability in single-cell RNA-Seq cell type discovery
Imputation-guided re-construction of complete methylomes from WGBS data
Imputation-guided re-construction of complete methylomes from WGBS data
Imputation-guided re-construction of complete methylomes from WGBS data
Imputation of label-free mass spectrometry peptides
Imputation of label-free mass spectrometry peptides
Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data
Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Inference And Analysis Of Synteny Networks
Inferring functionally related proteins using protein interaction networks
Inferring functionally related proteins using protein interaction networks
Inferring miRNA sponge modules in heterogeneous data
Inferring miRNA sponge modules in heterogeneous data
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Inferring the Tree of Cells
Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling
Inferring unobserved perturbations from gene expression data
Information Accretion-based Function Predictor Evaluation
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
Install/Update Bioconductor and CRAN Packages
Install/Update Bioconductor and CRAN Packages
Install/Update Bioconductor and CRAN Packages
Install/Update Bioconductor and CRAN Packages
Integrated Differential Expression and Differential Network Analysis (INDEED)
Integration of Disease Similarity Methods
Integration of Disease Similarity Methods
Integrative Analysis and Visualization of Epigenomic Sequencing Data
Integrative Analysis and Visualization of Epigenomic Sequencing Data
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of multi-omics data to infer regulatory networks
Integrative analysis of structural variations
Integrative analysis of structural variations
Integrative network analysis of omics data
Integrative network analysis of omics data
interactive analysis and visualization of alternative splicing in R
Interactive Cytometry Gating in R
Interactive Cytometry Gating in R
Interactive Differential Expression Analyzer
Interactive graphical application for clinical assessment of sequence coverage at the base-pair level
Interactive graphical application for clinical assessment of sequence coverage at the base-pair level
Interactive visualization and manipulation of nested networks
Interactive visualization in genomics
Interactive visualization in genomics
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
Interactive visualization of scRNA-seq data with Cerebro
Interactive Workflow for Discovering Rhythmicity in Biological Data
Interactive Workflow for Discovering Rhythmicity in Biological Data
InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Interpretation and enrichment for metabolomics data
Interpretation and enrichment for metabolomics data
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
iPath pipeline for detecting perturbed pathways at individual level
iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement
Isoform expression estimation based on RNA-seq data
iSTOP - Induced STOP Experiment Design
iSTOP - Induced STOP Experiment Design
Iterative Differential Clustering for single-cell
Iteratively Adjusted Surrogate Variable Analysis
Iteratively Adjusted Surrogate Variable Analysis
Iteratively Adjusted Surrogate Variable Analysis
Iterative Pruning to Capture Population Structure
Iterative Pruning to Capture Population Structure version 2
Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics
Judging Quality of Clustering Methods using Mutual Information
Judging Quality of Clustering Methods using Mutual Information
K-Mers Similarity Score Matrix
k-nearest neighbour batch effect test
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
Labels normalized cells for CyTOF data and assigns probabilities for each label
Landscape Expression Visualization Interface
Landscape Expression Visualization Interface
Landscape Single Cell Entropy
LC-MS/MS Differential Expression Tests
LEA: an R package for Landscape and Ecological Association Studies
Learning from DNA to Predict Enhancers
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
Library for (single-cell) SNP array processing
Linear model and normality based normalization and transformation method (Linnorm)
Linear Subpsace identification to solve complete gene expression deconvolution problem
LinkHD: a versatile framework to explore and integrate heterogeneous data
LinkHD: a versatile framework to explore and integrate heterogeneous data
LinkHD: a versatile framework to explore and integrate heterogeneous data
LinkHD: a versatile framework to explore and integrate heterogeneous data
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Long gene expression as a metric for neuronal identity
Longitudinal system suitability monitoring and quality control for proteomic experiments
Longitudinal system suitability monitoring and quality control for proteomic experiments
LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates
LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates
Maaslin
Maaslin2
Machine learning tools for automated transcriptome clustering analysis
MACS: Model-based Analysis for ChIP-Seq
Make Complex Heatmaps
Make Complex Heatmaps
Make Complex Heatmaps
Make Interactive Complex Heatmaps
Making 2D Hilbert Curve
Making 2D Hilbert Curve
Making 2D Hilbert Curve
Making Complex Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
Manages subsets of data with Bioconductor Experiment objects
Manages subsets of data with Bioconductor Experiment objects
Managing Expiration for Cache Directories
Mass Cytometry S4 Class Structure Pipeline for Images
Mass Cytometry S4 Class Structure Pipeline for Images
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
Massive and Integrative Gene Set Analysis
Massive and Integrative Gene Set Analysis
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Matched Interaction across Tissues (MIxT) data analysis
Maximum Likelihood Decay Modeling of RNA Degradation Data
Maximum Likelihood Decay Modeling of RNA Degradation Data
Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions
Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions
MBDDiff for processing MBDcap-seq datasets
Mean/Median-balanced quantile normalization
Mean/Median-balanced quantile normalization
Mean/Median-balanced quantile normalization
Mechanism-Aware Imputation
megadepth: BigWig and BAM related utilities
megadepth: BigWig and BAM related utilities
MeSH Enrichment and Semantic analyses
MeSH Enrichment and Semantic analyses
MeSH(Medical Subject Headings) Semantic Similarity Measures
Meta-analysis of Gene Set differential Co-expression Analysis
Metabolite Set Enrichment Analysis (MSEA)
Metabolomics Workbench in R
Metabolomics Workbench in R
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
MetaCyto: A package for meta-analysis of cytometry data
MetaCyto: A package for meta-analysis of cytometry data
Meta Gene Set Co-expression Analysis
MetFamily: Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies
Method for Combining LC-MS Metabolomics Feature Measurements
Method for Combining LC-MS Metabolomics Feature Measurements
Method for Combining LC-MS Metabolomics Feature Measurements
Methods for Single-Cell RNA-Seq Data Analysis
Methods for Single-Cell RNA-Seq Data Analysis
Methods for Spike-in Arrays
Methods for Spike-in Arrays
Methods for TCR single-cell embedding
Method to generate robust consensus from published cell deconvolution/aggregation methods
methometR: Extracting methylation information from Optical Genome Maps
Methylation Analysis Based on Signal Detection
MethylIT utility
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Microbial community dIversity and Network Analysis
Microbiome analysis
Microbiome analysis
Microbiome Analysis Plotting and Visualization
Microbiome Data Simulation
Microbiome differential abudance and correlation analyses with bias correction
Microbiome Differential Abundance Simulation
Microbiome Exploration App
Microbiome Exploration App
Microbiome Time Series Analysis
Mini-batch K-means Clustering for Single-Cell RNA-seq
Mini-batch K-means Clustering for Single-Cell RNA-seq
Minimal Protein Set Explaining Peptide Spectrum Matches
Minimal Protein Set Explaining Peptide Spectrum Matches
Minimized Single-Cell Consensus Clustering
Minimized Single-Cell Consensus Clustering
miRNAselector - a package for biomarker selection based on high-throughput experiments.
miRNAtap: microRNA Targets - Aggregated Predictions
mirTarRnaSeq
Missing Value Estimation of DNA Methylation Data
Mixtures of Matrix Variate Poisson-log Normal Distributions
Mixtures of Multivariate Poisson-Log Normal Model for Clustering Count Data
MLG Clustering
'(m,n)-mer' - A Simple Statistical Feature for Sequence Classification
Model based analysis for paired-end data
Model based analysis for paired-end data
Model-Based Comparative Analysis of the TCR Repertoire
Model-Based Comparative Analysis of the TCR Repertoire
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolite Profiles
Modified Concordance Index
Modified Concordance Index
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Molecular Signature identification using Biclustering
Motif Analysis In Gene Regulatory Networks
motif matching, comparison, and de novo discovery using the MEME Suite
motif matching, comparison, and de novo discovery using the MEME Suite
Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping
Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping
Multilevel Model for Multivariate Responses with Missing Values
Multi-locus multi-purpose Crispr/Cas design
Multiomic Batch effect Correction
Multiomic Batch effect Correction
Multi Omic Master Regulator Analysis
Multi Omic Master Regulator Analysis
Multi-omics Classification, Functional Enrichment and Network Inference analysis
Multi-Omics REgulation (MORE)
Multi-Omics Simulation (MOSim)
Multi-Omics Simulation (MOSim)
Multi-Omics (time-course) network-based integration and interpretation
Multiple co-inertia analysis of omics datasets
Multiple co-inertia analysis of omics datasets
Multiple omics data integrative clustering and gene set analysis
Multiple omics data integrative clustering and gene set analysis
Multiple Sample Peak Calling: Using combined evidence from replicates to evaluate ChIP-seq peaks
Multiplex PCR Primer Design and Analysis
Multiplex PCR Primer Design and Analysis
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Multi-Scale Target Explorer
"Multivariable Association Discovery in Population-scale Meta-omics Studies"
"Multivariable Association Discovery in Population-scale Meta-omics Studies"
Multivariate Information Criteria to identify important predictors in high dimensional multivariate regression
Multivariate Information Criteria to identify important predictors in high dimensional multivariate regression
Multiview Intercellular SpaTial modeling framework
Multiview Intercellular SpaTial modeling framework
Mutational Signature Comprehensive Analysis Toolkit
Mutational Signature Comprehensive Analysis Toolkit
nanotatoR: next generation structural variant annotation and classification
Negative binomial model for scRNA-seq
Negative binomial model for scRNA-seq
Negative Binomial Models to detect Differential Splicing
Negative Binomial Models to detect Differential Splicing
Neighbor_net analysis
netboxr
netboxr
Network Analysis Supported by Boosting
Network Centrality Metrics for Elastic-Net Regularized Models
Network Centrality Metrics for Elastic-Net Regularized Models
Network-Regularized Regression Models
NEUral network-based single-Cell Annotation tool
Next generation structural variant annotation and classification
Next generation structural variant annotation and classification
Non-detects in qPCR data
Non-detects in qPCR data
Non-detects in qPCR data
Non-parametric analysis of response curves for thermal proteome profiling experiments
Non-parametric analysis of response curves for thermal proteome profiling experiments
Non-parametric analysis of response curves for thermal proteome profiling experiments
Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data
Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data
Normalization of Single-Cell mRNA Sequencing Data
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Novel Mutational Signature Analysis
Object design (S4) for AMARETTO
Obtain Raw Read Counts from RNASeq Data
Obtain Raw Read Counts from RNASeq Data
Omics-Based Interaction Framework
OmicSelector - a package for biomarker selection based on high-throughput experiments.
Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies
OmniPath web service client
OmniPath web service client and more
OnASSIs Ontology Annotation and Semantic SImilarity software
OnASSIs Ontology Annotation and Semantic SImilarity software
One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)
One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)
One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)
Online error control
Online error rate control
ontology enrichment analysis
OpenAccess TCGA Data on Terra as MultiAssayExperiment
OpenAccess TCGA Data on Terra as MultiAssayExperiment
Open Cancer TherApeutic Discovery (OCTAD)
Open Cancer TherApeutic Discovery (OCTAD)
Open Cancer TherApeutic Discovery (OCTAD)
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Open Reading Frames in Genomics
optimalFlow
optimalFlow
Optimising the Definition of Expressed Regions
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized LC-MS Spectra Processing
Outlier-aware and Count-based Compositional Analysis of Single-cell Data.
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
OVESEG-test to detect tissue/cell-specific markers
OVESEG-test to detect tissue/cell-specific markers
Package analyse 4C sequencing data
Package for CTDbase data query, visualization and downstream analysis
Package for CTDbase data query, visualization and downstream analysis
Package for Fold-specific GO Terms Recognition
Package for Fold-specific GO Terms Recognition
Package for Fold-specific GO Terms Recognition
Package for Single-cell Data Visualization and Analysis
Package pour l'introduction à la visualisation en R
Package to Perform High Throughput Biological Screening
Package to work with miRNAs and miRNA targets with R
PaIRKAT
Pancreatic Ductal Adenocarcinoma Tool-Kit
Pancreatic Ductal Adenocarcinoma Tool-Kit
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
Pathway Enrichment Based on Differential Causal Effects
Pathway Enrichment Based on Differential Causal Effects
Pathway enrichment using a regularized regression approach
Pathway Fingerprint Framework in R
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Peak Matrix Processing and signal batch correction for metabolomics datasets
Peak Matrix Processing and signal batch correction for metabolomics datasets
Peak Refinement Metric Gathering and Evalutation by Motif Enrichment
Peak saturation processing and analysis
Perform a maximum contrast projection of 3D images along the z-dimension into 2D
Perform a maximum contrast projection of 3D images along the z-dimension into 2D
Perform methylation analysis
Perform methylation analysis and facilitates differential expression analyses
Perform Needleman-Wunsch algorithm
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
Permutation filtration for microbiome data
Permutation filtration for microbiome data
Phase template strands from Strand-seq data
PhenoGeneRanker: A gene and phenotype prioritization tool
Phenotype-driven module identification
Phenotype-driven module identification
Phenotyping of microbial Raman spectroscopy data
Phylogenetic partitioning based ILR transform for metagenomics data
Phylogenetic partitioning based ILR transform for metagenomics data
Phylogenetic Reconstruction and Analysis
Phylogenetic Reconstruction and Analysis
Phylogeny-based sequence clustering with site polymorphism
Phylogeny-based sequence clustering with site polymorphism
PhyloProfile
PhyloProfile
PhyloProfile
PhyloProfileCorona
PhyloProfileRibi
Pipeline for augmented co-expression analysis
Pipeline for augmented co-expression analysis
Pipeline for identifying LINE1 insertoin in the WGS data
Pipeline for single cell multi-omic data pre-processing
pipeline for single cell RNA-seq data analysis
Pipeline framework for bioinformatics in R
Pipeline framework for bioinformatics in R
PIVOT launcher
Placental DNA methylation analysis tools
Placental DNA methylation analysis tools
PLNet: Sparse precision matrix estimation via lasso penalized D-trace loss in the multivariate Poisson log-normal model
PLNet: Sparse precision matrix estimation via lasso penalized D-trace loss in the multivariate Poisson log-normal model
Plot Gene Ontology and KEGG pathway Annotation and Abundance
Plot Multiple Sequence Alignment using 'ggplot2'
Plots of Statistics Collected by Qualimap from RNASeq Data
Plot the effect of one omics data on other omics data along the chromosome
Plot the effect of one omics data on other omics data along the chromosome
Plotting functions for derfinder
Plotting functions for derfinder
Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections
Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections
PolyA counting and differential transcript usage analysis for scRNA-seq data
Pooling RNA-seq datasets for assembling transcript models
Pooling RNA-seq datasets for assembling transcript models
Population-Specific Expression Analysis.
Population-Specific Expression Analysis.
Position Related Data Analysis
Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
preciseTAD: A machine learning framework for precise TAD boundary prediction
preciseTAD: A machine learning framework for precise TAD boundary prediction
preciseTAD: A machine learning framework for precise TAD boundary prediction
Predict Combined Function of Transcription Factors
Predict genes expressed selectively in specific cell types
Predict genes expressed selectively in specific cell types
Predicting Targets for Drosophila Intragenic miRNAs
Predicting Targets for Drosophila Intragenic miRNAs
Prediction of intronic splicing branchpoints
Prediction of intronic splicing branchpoints
Predicts the genome build version of genomic track files
Predict transcription factor occupancy using DNase- or ATAC-seq data
Pre-process 1H-NMR FID signals
Pre-process 1H-NMR FID signals
Pre-process 1H-NMR FID signals
Pre-process 1H-NMR FID signals
Pre-process 1H-NMR FID signals
Pre-process DNA Copy Number (CN) Data for Detection of CN Events
Preprocessing of spectra data from high resolution mass spectrometry
Pre-processing PTR-TOF-MS Data
Pretrained learning models for cell type prediction on single cell RNA-sequencing data
Pretrained learning models for cell type prediction on single cell RNA-sequencing data
Prize: an R package for prioritization estimation based on analytic hierarchy process
Probe-level Expression Change Averaging
Processing of adductomic mass spectral datasets
Processing of adductomic mass spectral datasets
Processing Various Types of Data on GEO and TCGA
Profiles and targets subpopulations with high Treatment EEFects
Profile score distributions
Protein co-expression network analysis (ProCoNA).
Protein co-expression network analysis (ProCoNA).
Protein Interactions and Networks with Compounds based on Sequences using Deep Learning
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).
Provide methods for microarray analysis
Provides a GUI for DAPAR
Provides helper functions for microbiome preprocessing and analysis
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
Publish Packages and Other Resources to AnVIL Workspaces
Publish Packages and Other Resources to AnVIL Workspaces
PWM enrichment analysis
QC for enrichment based NGS
QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.
QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.
Quality Control for Single-Cell RNA-seq Data
Quality Control for Single-Cell RNA-seq Data
Quality Control for Single-Cell RNA-seq Data
Quantification of the Tumor Immune contexture from RNA-seq data
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantify and interpret drivers of variation in multilevel gene expression experiments
Quasispecies Diversity
Quasispecies Diversity
qusage: Quantitative Set Analysis for Gene Expression
qusage: Quantitative Set Analysis for Gene Expression
Randomize Samples for -omics Profiling
Random Rotation Methods for High Dimensional Data with Batch Structure
Random Rotation Methods for High Dimensional Data with Batch Structure
Rank-based single-sample gene set scoring method
Rank-based single-sample gene set scoring method
Rank Constrained Similarity Learning for single cell RNA sequencing data
Rank Constrained Similarity Learning for Single Cell RNA Sequencing Data
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr
Rapid Reconstruction of Time-Varying Gene Regulatory Networks
Rapid Reconstruction of Time-Varying Gene Regulatory Networks
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
R Client for Seven Bridges Genomics API (v1)
Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers
Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers
Recipes using seqsetvis
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Reference-Based Single-Cell RNA-Seq Annotation
Reference-Based Single-Cell RNA-Seq Annotation
Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data
Reference-guided isoform reconstruction and quantification for long read RNA-Seq data
Refitting diploid region profiles using a clustering procedure
Refitting diploid region profiles using a clustering procedure
Regression Models with Multivariate Outcomes for Mass Cytometry Experiments
Remove Unwanted Variation from RNA-Seq Data
Remove Unwanted Variation from RNA-Seq Data
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
Representing Different Biological Sets
Representing Different Biological Sets
Representing Different Biological Sets
Representing Different Biological Sets
Reproducibility-Optimized Test Statistic
Retrieve and analyze data from the Human Protein Atlas
Retrieve and analyze data from the Human Protein Atlas
Retrieve and analyze data from the Human Protein Atlas
Reusable and reproducible Data Management
Re-using Content in Bioconductor Books
Re-using Content in Bioconductor Books
Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data
Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data
R functions
RiboseQC, a Comprehensive Ribo-Seq Analysis Tool
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
'rifi' analyses data from rifampicin time series created by microarray or RNAseq
R implementation of informtion measures
R implementation of the LEfSE method for microbiome biomarker discovery
R implementation of the LEfSE method for microbiome biomarker discovery
RNA Centric Annotation System
RNA Centric Annotation System
RNA-seq analysis using multiple algorithms
RNA-seq analysis using multiple algorithms
RNAseq and qPCR signal comparison
RNA-seq workflows at HCI
Robust differential co-expression test by copula
Robust Inference for Absolute Abundance in Microbiome Analysis
Robust Inference for Absolute Abundance in Microbiome Analysis
Robust Inference for Absolute Abundance in Microbiome Analysis
Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data
Robust prediction of clinical outcomes using cytometry data without cell gating
Robust prediction of clinical outcomes using cytometry data without cell gating
Robust statistical inference for quantitative LC-MS proteomics
Rothstein Lab SGA Analysis Tools
R package for analysing TFBSs in DNA sequences
R package for CRAG
R package for CRAG
R package for Manhattan Plots
R package for Manhattan Plots
R Package for Processing High Content Screening data
R Package for Processing High Content Screening data
R Package for Processing High Content Screening data
R package for sparse and out-of-core arithmetic and decomposition of Tensor
R package motivated by the SCTC Dream Challenges
R package of gene set enrichment analysis
R Package Template - Enhanced
R SDK for BaseSpace RESTful API
R SeqAn
R Tools for RNA-Seq Projects at Institut Pasteur (Biomics Platform)
Run workflows implemented in Terra/AnVIL workspace
`rutils` is a home for my commonly used R utility functions
R Wrapper for DGIdb
R Wrapper for DGIdb
R wrapper for Progenetix
R wrapper for SpatialDE
R wrapper for the OMA REST API
R wrapper for the OMA REST API
R wrapper for the OMA REST API
R wrapper for the OMA REST API
R wrapper for the python openTSNE library
R wrapper for the python openTSNE library
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
SAFE-clustering:Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data
SAME: Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble for Single-cell RNA-seq Data
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs
Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies
Scaling normalization based on the Pareto distribution
SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction
Science-wise false discovery rate and proportion of true null hypotheses estimation
Science-wise false discovery rate and proportion of true null hypotheses estimation
Science-wise false discovery rate and proportion of true null hypotheses estimation
Scientific Data on Time of Lineage Divergence for Your Taxa
Scientific Data on Time of Lineage Divergence for Your Taxa
Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences
scMerge: Merging multiple batches of scRNA-seq data
scMerge: Merging multiple batches of scRNA-seq data
scReClassify: post hoc cell type classification of single-cell RNA-seq data
scRecover for imputation of single-cell RNA-seq data
scRecover for imputation of single-cell RNA-seq data
scRecover for imputation of single-cell RNA-seq data
scRMD: Imputation for single cell RNA-seq data via robust matrix decomposition
scRMD: Imputation for single cell RNA-seq data via robust matrix decomposition
ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion
Secondary analyses of CNV data (HRD and more)
Selecting the number of mutational signatures using a perplexity-based measure and cross-validation
Selecting transcript model using PRO-seq
Set Based Visualizations for Next-Gen Sequencing Data
Set Based Visualizations for Next-Gen Sequencing Data
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering
Shiny Application for Multiplex PCR Primer Design and Analysis
Shiny Application for Multiplex PCR Primer Design and Analysis
Shiny interface for Cardinal
SIAT: Symptom Intensity Tool Analysis
SIAT: Symptom Intensity Tool Analysis
Signal batch correction for (LC)-MS data
Signature Overrepresentation Analysis
signet: Selection Inference in Gene NETworks
signet: Selection Inference in Gene NETworks
Significance Analysis of Function and Expression
Significance Analysis of Function and Expression
SIMD Partial Order Alignment in R
Similar Binding Profiles
Similarity measures for chemical compounds
Simple Demo of S4 Methods and Classes for Bioconductor
Simple, sequence-based simulation of epi-genomes.
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
simple Two-Tier Mapper: an interface for Two-Tier Mapper
Simplify Functional Enrichment Results
Simplify Functional Enrichment Results
Simplify Functional Enrichment Results
Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
Simulating Multi-omics Datasets with Arbitrary Association Structure
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulation of Rare Variant Genetic Data
Simulation, power evaluation, and sample size recommendation for single cell RNA-seq
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
SINCE - a robust algorithm for single-cell number of clusters estimation
Single-cell analysis toolkit for gene expression data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Batch Correction Methods
Single-Cell Batch Correction Methods
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation
Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation
Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation
Single Cell Differential Expression
Single Cell Differential Expression
Single Cell Entropy
single-cell higher order testing
single-cell higher order testing
Single Cell Inference of Regulatory Activity
Single-Cell Operation for Neat Enrichment
Single Cell Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Single-Cell RNA-Seq Analysis Utilities
Single-Cell RNA-Seq Analysis Utilities
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single-cell Targetted Network Inference
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Single Nucleus Analysis Package for ATAC-Seq
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Singular Value Decomposition for Bioconductor Packages
Singular Value Decomposition for Bioconductor Packages
Small-Count Analysis Methods for High-Dimensional Data
Small-Count Analysis Methods for High-Dimensional Data
SMNN: Batch Effect Correction for Single-cell RNA-seq data with Supervised Mutual Nearest Neighbor Detection
SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
some skill for me (Title Case)
Sparse Data Observations for Simulating Synthetic Abundance
Sparse Data Observations for Simulating Synthetic Abundance
Spatial Image Analysis of Tissues
Spatial Transcriptomics Analysis
Spatial Transcriptomics Analysis
SpectralTAD: Hierarchical TAD detection using spectral clustering
SpectralTAD: Hierarchical TAD detection using spectral clustering
SpectralTAD: Hierarchical TAD detection using spectral clustering
SQANTI Explorer
SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data
SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data
ssPATHS: Single Sample PATHway Score
ssPATHS: Single Sample PATHway Score
ssPATHS: Single Sample PATHway Score
S-system parameter estimation method
Stabilised mosaic single cell data integration using unshared features
stageR: stage-wise analysis of high throughput gene expression data in R
stageR: stage-wise analysis of high throughput gene expression data in R
Standardize Antibody Names
Standard styles for vignettes and other Bioconductor documents
Standard styles for vignettes and other Bioconductor documents
Standard styles for vignettes and other Bioconductor documents
Stan implementation of BASiCS
StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub
StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical Analysis of Metabolomic Data
Statistical Analysis of Molecular Profiles
Statistical Analysis of Molecular Profiles
Statistical Analysis of MPRA data
Statistical Analysis of MPRA data
Statistical Analysis of RNA-Seq Tools
Statistical analysis of sequins
Statistical analysis of sequins
Statistical approaches for differential expression analysis in metatranscriptomics
Statistical Characterization of Post-translational Modifications
Statistical Characterization of Post-translational Modifications
Statistical Characterization of Post-translational Modifications
Statistical Characterization of Post-translational Modifications
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)
Statistical Modelling of AP-MS Data (SMAD)
Statistical Modelling of AP-MS Data (SMAD)
Statistical Testing for ChIP-Seq data sets
Statistical Testing for ChIP-Seq data sets
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
stJoincount - Join count statistic for quantifying spatial correlation between clusters
Store and plot TFBS sites from HOCOMOCO v11 scored by FIMO
Storing and accessing epitranscriptomic information using the AnnotationDbi interface
Storing and accessing epitranscriptomic information using the AnnotationDbi interface
Structure Learning for Count Data
Submitter and Monitor of the 'LSF Cluster'
Submitter and Monitor of the 'LSF Cluster'
Subtype Identification with Survival Data
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
Summary Statistics for Rows and Columns of Sparse Matrices
Summary Statistics for Rows and Columns of Sparse Matrices
Support for Springer monograph on Bioconductor
supraHex: a supra-hexagonal map for analysing tabular omics data
supraHex: a supra-hexagonal map for analysing tabular omics data
supraHex: a supra-hexagonal map for analysing tabular omics data
SVM2CRM: support vector machine for cis-regulatory elements detections
SVM2CRM: support vector machine for cis-regulatory elements detections
SWATH extended library generation and statistical data analysis
Switch-like differential expression across single-cell trajectories
Switch-like differential expression across single-cell trajectories
Synteny Alignment and Analysis for Saccharomyces sensu stricto
Systematic quality checks on comparative genomics analyses
Systems EPigenomics Inference of Regulatory Activity
Systems EPigenomics Inference of Regulatory Activity
System-wise protein turnover curve fitting
TADCompare: Identification and characterization of differential TADs
TADCompare: Identification and characterization of differential TADs
TADCompare: Identification and characterization of differential TADs
TARgeted SEQuencing Experiment Quality Control
TARgeted SEQuencing Experiment Quality Control
Target Inhibition Interaction using Maximization and Minimization Averaging
taxFun
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGA utility functions for data management
TCGA utility functions for data management
TCGA utility functions for data management
TCGA utility functions for data management
Ternary Network Estimation
Ternary Network Estimation
Test branch renaming
Test, Document, Containerise, and Deploy R Packages
Test for differential expression for RNA-seq data
Testing AnnHub transition to Azure
Testing multiple biological mediators simultaneously
Testing multiple biological mediators simultaneously
Test Single Package Builder
Test Single Package Builder
text mining for msigdb sets construed as documents
The Cancer Genome Atlas Data Integration
The Cancer Genome Atlas Data Integration
The Herper package is a simple toolset to install and manage conda packages and environments from R
The Herper package is a simple toolset to install and manage conda packages and environments from R
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
Thermal proximity co-aggregation with R
Thermal proximity co-aggregation with R
the R package for analyzing expression evolution based on RNA-seq data
The slim version of signac
The subREgion-based BurdEn Test (REBET)
This package is a single-cell ATAC-seq simulator
This R package for performing module repertoire analyses and generating fingerprint representations
Tidy Meta Profiles using Bioconductor and the Tidyverse
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Time sensitive microRNA-mRNA integration, analysis and network generation tool
Time sensitive microRNA-mRNA integration, analysis and network generation tool
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Tokenizing Text of Gene Set Enrichment Analysis
Tools for analysing methylation patterns at genomic tuples
Tools for Connectivity Map-like analyses
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
Tools for high-throughput metabolomics
Tools for high-throughput metabolomics
Tools for making reports in various formats
Tools for making reports in various formats
Tools for Manipulating the FOBI Ontology
Tools for Manipulating the FOBI Ontology
Tools for Manipulating the FOBI Ontology
Tools for matrices with precision weights, test and explore weighted or sparse data
Tools for matrices with precision weights, test and explore weighted or sparse data
Tools for Metabolomics Data
Tools for Metabolomics Data
Tools for Omics Data Analysis
Tools for Omics Data Analysis
Tools for ordering single-cell sequencing
Tools for ordering single-cell sequencing
Tools for processing of high-dimensional cytometry data
Tools for processing of high-dimensional cytometry data
Tools for spliced gene structure manipulation and analysis
Tools for spliced gene structure manipulation and analysis
Tools for the Efficient Analysis of High-Resolution Genomics Data
Tools for the Efficient Analysis of High-Resolution Genomics Data
Tools for working with diverse immune genes
Tools for working with ScreenMill data
Tools to aid the development of Bioconductor Workflow packages
Tools to aid the development of Bioconductor Workflow packages
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells.
Tools to assess and compare miRNA expression estimatation methods
Tools to assess and compare miRNA expression estimatation methods
Tools to assess and compare miRNA expression estimatation methods
Tools to query the Bioconductor package binary repositories.
trajectory-based differential expression analysis for sequencing data
trajectory-based differential expression analysis for sequencing data
Trajectory functions for visualization and interpretation.
Transcript Annotation Tool (TransAT): an R package for retrieving annotations for transcript specific genetic variants
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
Transcriptional Data Guided fMRI Network Classification
Transcription Factor High Accumulation Zones
Transcription Factor High Accumulation Zones
Transcription Factors Enrichment Analysis
Transcription Factors Enrichment Analysis
Transcriptomic Ovarian Cancer Datasets
Transcriptomic Ovarian Cancer Datasets
Tree Aggregation
tricycle: Transferable Representation and Inference of cell cycle
TSS sequencing data analysis
Tumor Mutational Burden Quantification From Gene Panels And WES
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
Two-Tier Mapper: a clustering tool based on topological data analysis
Two-Tier Mapper: a clustering tool based on topological data analysis
Unified Statistal Modeling of Omics Data
Unified Statistal Modeling of Omics Data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unlocking iSEE for transcript-level visualization
Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
Untargeted LC-MS data annotation
uORF prediction in R
Useful bioinformation tools for R.
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
User-friendly Workflow for Pre-processing and Statistical Analysis of Mass Spectrometry Data
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Using self-organizing maps for visualization and interpretation of cytometry data
Using self-organizing maps for visualization and interpretation of cytometry data
Using self-organizing maps for visualization and interpretation of cytometry data
Using TileDB as a DelayedArray Backend
Using TileDB as a DelayedArray Backend
Utilities for handling genomic interaction data
Utilities for handling genomic interaction data
Utilities for handling genomic interaction data
Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.
Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.
Utilities to create and use Bioconductor Hubs
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation
Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation
Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation
Variable Selection Oriented LASSO Bagging Algorithm
Variable Selection Oriented LASSO Bagging Algorithm
Variable Selection Oriented LASSO Bagging Algorithm
Variance Adaptive Shrinkage
Varying-Censoring Aware Matrix Factorization
View AnnotationHub and ExperimentHub Resources Interactively
View AnnotationHub and ExperimentHub Resources Interactively
Viscello for Visualization of Single Cell Data
Viscello for Visualization of Single Cell Data
Viscello for Visualization of Single Cell EHT Data
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity
Visual comparison of mutational processes in a set of tumors
Visual Exploration of Omic Datasets Using a Shiny App
Visual Exploration of Omic Datasets Using a Shiny App
Visual Exploration of Omic Datasets Using a Shiny App
Visualise methlation data from Oxford Nanopore sequencing
Visualise methlation data from Oxford Nanopore sequencing
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualising Set Enrichment Analysis Results
Visualising Set Enrichment Analysis Results
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result
Visualization of genomic structural variants
Visualization of highly multiplexed imaging data in R
Visualization of highly multiplexed imaging data in R
Visualization of highly multiplexed imaging data in R
Visualization of Phylogenetic Networks
Visualization of Phylogenetic Networks
Visualization Tool for Genetic Reassortment
Visualization Tool for Sequence Recombination and Reassortment
Visualizing Structure in ecological site-species abundance data
Weighting protein-protein interactions
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
What the Package Does (TODO)
What the Package Does TODOELI
Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data
Workflow to process tandem MS files and build MassBank records
Workflow to process tandem MS files and build MassBank records
Working with modified nucleotide sequences
Working with modified nucleotide sequences
Wrench normalization for sparse count data
Wrench normalization for sparse count data
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
Yet Another Single-Cell Analysis Toolkit (Yeskit)
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Zwyx