Biocview "Software"

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
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
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 Scalable and Flexible Non Negative Matrix Factorization Method
Affinity test for identifying regulatory SNPs
Affinity test for identifying regulatory SNPs
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 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 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
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 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 Copy Number Variation in Single-Cell-Sequencing Data
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Analysis Of Differential Abundance Taking Sample 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 Pharmacogenomic Data
Analysis of Large-Scale Pharmacogenomic Data
Analysis of Large-Scale Radio-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 Epigenomic data in a Shiny App
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 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 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.
Annotate sequences with KEGG pathways
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 of Optical Mapping Structural variants
Annotation of Optical Mapping Structural variants
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
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 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 analysis, visualization and biomarker discovery of microbiome
an R package for analysis, visualization and biomarker discovery of microbiome
an R package for analysis, visualization and biomarker discovery of microbiome
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 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 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 simulate DNA methylation data
A package for visualizing complex biological network
A package of creating an algorithm of identifying microRNA-competing endogenous RNA triplets
Application of t-sne to NGS Genomic Signal Profiles
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 Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
A Shiny App to accompany clusterExperiment
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
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 **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
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 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 tool to calculate and validate primers for Golden Gate Cloning
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, probabilistic assignment of scRNA-seq to cell types
Automated spectraL Processing System for NMR
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
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
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 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)
BEAT - BS-Seq Epimutation Analysis Toolkit
Bias-free Footprint Enrichment Test
Bias-free Footprint Enrichment Test
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Binomial Random Forest Feature Selection
Binomial Random Forest Feature Selection
biodb, a library and a development framework for connecting to chemical and biological databases
biodbChebi, a library for connecting to the ChEBI Database
biodbHmdb, a library for connecting to the HMDB Database
biodbKegg, a library for connecting to the KEGG Database
biodbUniprot, a library for connecting to the Uniprot Database
Bioinformatics pipelines based on Rcwl
Bioinformatics pipelines based on Rcwl
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
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
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
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-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
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
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-seq data from ALL samples
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
Client for GREAT Analysis
Clonal ordering and visualization
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 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
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 Bioc 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.
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compensates for the bias introduced by median normalization in phosphoproteomics
CompositeDriver
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Compute coverage matrices from recount quickly using bwtool
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
Convex Analysis of Mixtures for Tissue Heterogeneity Characterization
Convex Analysis of Mixtures for Tissue Heterogeneity Characterization
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
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
Correspondence Analysis for Single Cell Data
Coverage visualization package for R
Create 3D transomics network view with Çytoscape and Cy3D
Creates and uses physio spaces as a dimension reduction mapping
Creates diffusion maps
Creates diffusion maps
crisprseekplus
crisprseekplus
CUE: CpG impUtation Ensemble for DNA Methylation Levels Across the HumanMethylation450 (HM450) BeadChip and HumanMethylation EPIC (HM850) BeadChip Platforms
Cutsomize and Query Compound Annotation Database
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
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
DegNorm: degradation normalization for RNA-seq data
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
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 different methylation level (DMR)
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 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
Detection of site fixation in molecular evolution
Detection of sites with fixation of amino acid substitutions in protein evolution
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
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
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
Differentially Methylated Regions caller
Differentially Methylated Regions caller
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
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
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
doseLM
doseR
doseR
doseR
doseR
doseR
doseR
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
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
EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices
EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices
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
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
EpiMethEx Package
Epistasis Analysis for Quantitative Traits by Functional Regression Model
Eric Utilities
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
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 recount project
Explore and download data from the recount project
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
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 calculation of uniConSig and CSEA
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
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
Finding Mutually Exclusive Groups of Alterations in Cancer Datasets
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 re-gions from Hi-C data
Fit a Gamma-Poisson Generalized Linear Model
Fit a Gamma-Poisson Generalized Linear Model
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
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 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
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 Summary Plots of FastQC Reports
Generate synthetic nucleosome maps
Generate synthetic nucleosome maps
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
Generic Omics Pathway Enrichment Analysis
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
Genomic Knowledge-guided Multiple Testing
GenomicOperations
GenomicOperations
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
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
Graphical User Interface for IsoCorrectoR
Graphical User Interface for IsoCorrectoR
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
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
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
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 interaction networks and modules
Identification and analysis of miRNA sponge interaction networks and modules
Identification and Annotation of Protein Hotspot Residues
Identification and Annotation of Protein Hotspot Residues
Identification of genetic Variants affecting Alternative Splicing
ILoReg enables high-precision cell population identification from scRNA-Seq data
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
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 Omnipath network
Import Omnipath network
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
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
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
Inferring functionally related proteins using protein interaction networks
Inferring functionally related proteins using protein interaction networks
Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
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 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 structural variations
Integrative analysis of structural variations
Integrative network analysis of omics data
Integrative network analysis of omics data
Interactive Differential Expression Analyzer
Interactive graphical application for clinical assessment of sequence coverage at the base-pair level
Interactive visualization and manipulation of nested networks
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
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
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
Isoform expression estimation based on RNA-seq data
iSTOP - Induced STOP Experiment Design
iSTOP - Induced STOP Experiment Design
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
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
Landscape Expression Visualization Interface
Landscape Single Cell Entropy
LC-MS/MS Differential Expression Tests
LEA: an R package for Landscape and Ecological Association Studies
LeAFtool: Lesion Area Finding tool
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
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
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
Maaslin2
Maaslin2
Make Complex Heatmaps
Make Complex Heatmaps
Make 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
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
MeSH Enrichment and Semantic analyses
MeSH Enrichment and Semantic analyses
MeSH(Medical Subject Headings) Semantic Similarity Measures
Metabolite Set Enrichment Analysis (MSEA)
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
MetFamily: Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies
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
Method to generate robust consensus from published cell deconvolution/aggregation methods
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
Microbiome Differential Abundance Simulation
microRNA-mRNA Integration, Analysis and Network Generation Tool
Mini-batch K-means Clustering for Single-Cell RNA-seq
Mini-batch K-means Clustering for Single-Cell RNA-seq
Minimized Single-Cell Consensus Clustering
Minimized Single-Cell Consensus Clustering
miRNAselector - a package for biomarker miRNA selection based on miRNA-seq NGS data.
miRNAtap: microRNA Targets - Aggregated Predictions
Missing Value Estimation of DNA Methylation Data
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
Multilevel Model for Multivariate Responses with Missing Values
Multiomic Batch effect Correction
Multi Omic Master Regulator Analysis
Multi Omic Master Regulator Analysis
Multi-Omics Simulation (MOSim)
Multi-Omics Simulation (MOSim)
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
Multivariate Information Criteria to identify important predictors in high dimensional multivariate regression
Multivariate Information Criteria to identify important predictors in high dimensional multivariate regression
nanotatoR: next generation structural variant annotation and classification
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
Network-Regularized Regression Models
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
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
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 control
ontology enrichment analysis
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Open Reading Frames in Genomics
optimalFlow
optimalFlow
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq 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 to work with miRNAs and miRNA targets with R
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
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
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
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
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
PhyloProfile
PhyloProfile
PhyloProfile
pinnacle: Gene set enrichment analysis based on genomic intervals
Pipeline for augmented co-expression analysis
pipeline for single cell RNA-seq data analysis
pipeline for single cell RNA-seq data analysis
Pipeline framework for bioinformatics in R
Pipeline framework for bioinformatics in R
PIVOT launcher
Plot Gene Ontology and KEGG pathway Annotation and Abundance
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
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
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
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
Produces Summaries and Plots of Features Distributed Across Genomes
Profile score distributions
Protein co-expression network analysis (ProCoNA).
Protein co-expression network analysis (ProCoNA).
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
Provide methods for microarray analysis
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
PWM enrichment analysis
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
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantify and interpret divers 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
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 Product method for identifying differentially expressed genes with application in meta-analysis
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
Reference-Based Single-Cell RNA-Seq Annotation
Reference-Based Single-Cell RNA-Seq Annotation
Reference Index for Cell Types
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
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
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 prediction of clinical outcomes using cytometry data without cell gating
Robust prediction of clinical outcomes using cytometry data without cell gating
Rothstein Lab SGA Analysis Tools
R package for analysing TFBSs in DNA sequences
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 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 Wrapper for DGIdb
R Wrapper for DGIdb
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
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 Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies
SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
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
scMerge: Merging multiple batches of scRNA-seq data
scMerge: Merging multiple batches of scRNA-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
Selecting the number of mutational signatures using a perplexity-based measure and cross-validation
Selecting transcript model using PRO-seq
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 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
signet: Selection Inference in Gene NETworks
signet: Selection Inference in Gene NETworks
Significance Analysis of Function and Expression
Similar Binding Profiles
Similarity measures for chemical compounds
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
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
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 Batch Correction Methods
Single-Cell Batch Correction Methods
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single Cell Differential Expression
Single Cell Differential Expression
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 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 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
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
S-system parameter estimation method
stageR: stage-wise analysis of high throughput gene expression data in R
stageR: stage-wise analysis of high throughput gene expression data in R
Standard styles for vignettes and other Bioconductor documents
Standard styles for vignettes and other Bioconductor documents
Standard styles for vignettes and other Bioconductor documents
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 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 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
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
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
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
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
TARgeted SEQuencing Experiment Quality Control
TARgeted SEQuencing Experiment Quality Control
Target Inhibition Interaction using Maximization and Minimization Averaging
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 for differential expression for RNA-seq data
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 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
the R package for analyzing expression evolution based on RNA-seq data
The subREgion-based BurdEn Test (REBET)
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 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
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 high-throughput metabolomics
Tools for high-throughput metabolomics
Tools for making reports in various formats
Tools for making reports in various formats
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 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
trajectory-based differential expression analysis for sequencing data
trajectory-based differential expression analysis for sequencing data
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
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 Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
uORF prediction in 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
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
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 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
Variance Adaptive Shrinkage
Varying-Censoring Aware Matrix Factorization
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 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 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
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result
Visualization of highly multiplexed imaging cytometry data in R
Visualization of highly multiplexed imaging cytometry data in R
Visualization of highly multiplexed imaging cytometry data in R
Visualization of Phylogenetic Networks
Visualization of Phylogenetic Networks
Visualization Tool for Sequence Recombination and Reassortment
Visualization Tool for Sequence Recombination and Reassortment
Visualizing Structure in ecological site-species abundance data
Weighted matrix manipulation, finding components of variation with weighted or sparse data
Weighted matrix manipulation, finding components of variation with weighted or sparse data
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
Wrap Command Tools and Pipelines Using CWL
Wrap Command Tools and Pipelines Using CWL
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
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Zwyx