Biocview "Software"

Access HDF5 content from h5serv
Access HDF5 content from h5serv
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 and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions
A Correction Algorithm For Natural Isotope Abundance Contributions
Adaptive Signature Selection and InteGratioN (ASSIGN)
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 Framework for Quality Control
A Framework for Quality Control
A Framework for Quality Control
A framework for rapid prototyping with binary data on disk
A framework for rapid prototyping with binary data on disk
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 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
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
A mass spectrometry imaging toolbox for statistical analysis
A mass spectrometry imaging toolbox for statistical analysis
An algorithm for gene and gene set network inference
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 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 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 high-throughput microscopy-based screens
Analysis of Large-Scale Pharmacogenomic Data
Analysis of Large-Scale Pharmacogenomic Data
Analysis of Large-Scale Pharmacogenomic Data
Analyze comorbidities from electronic health record data
Analyze flow cytometric data using gate information
Analyze flow cytometric data using gate information
Analyze flow cytometric data using histogram information
Analyze flow cytometric data using histogram information
Analyze Gene Sets 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
An Implementation of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection
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 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 integrated analysis package of miRNA and mRNA expression data
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
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 interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
An Iteractive Consensus Clustering Framework for Multi-platform Data Analysis
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-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
Annotation and gene expression data retrieval from Bgee database
Annotation of Genomic Regions to Genomic Annotations
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
Annotation translation functions
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 package for identification of novel peptides by customized database derived from RNA-Seq
An R interface to the Ontology Lookup Service
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 subset-based association analysis of heterogeneous traits and subtypes
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 creation of complex genomic profile plots
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 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 and annotation of phylogenetic trees with their covariates and other associated data
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
An R package to simulate DNA methylation data
A package for visualizing complex biological network
A package for visualizing complex biological network
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 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 Properties to TNBC Patients
Assign rfPred functional prediction scores to a missense variants list
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 suite of functions to facilitate zFPKM transformations
A SummarizedExperiment for Ivy-GAP data
A SummarizedExperiment for Ivy-GAP data
Atlas and Analysis of Expert-Curated Pathways
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 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 tool for unsupervised projection of single cell RNA-seq 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
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 Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Automatically Aggregating and Summarizing lncRNA Analysis Results for Interactive Report
Automatically Aggregating and Summarizing lncRNA Analysis Results for Interactive Report
Automatic Statistical Identification in Complex Spectra
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
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
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 Compositional Covariance
Bayesian Analysis of Differential Expression in RNA Sequencing Data
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 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
BEAT - BS-Seq Epimutation Analysis Toolkit
Bias-free Footprint Enrichment Test
Bias-free Footprint Enrichment Test
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
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 growth-rate inhibition (GR) metrics
Cancer mutation analysis
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 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
Candidate gene prioritization based on convergent evidence
ccrepe_and_nc.score
ccrepe_and_nc.score
cell counter
Cell-Cycle using Mixture Models
Check Yeast Deletion Barcodes
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
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.
chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.
Chromosome Instability Index
Chromosome Instability Index
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 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
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
Client for GREAT Analysis
Clonal ordering and visualization
Clone and Donor Identification from Single Cell Data
Clone and Donor Identification from Single Cell 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 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.
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
Code for using BridgeDb identifier mapping framework from within R
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 Analysis of Sequencing Data
co-expression of lincRNAs and protein-coding genes
co-expression of lincRNAs and protein-coding genes
co-expression of lincRNAs and protein-coding genes
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
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
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
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
Compare Clusterings for Single-Cell Sequencing
Compensates for the bias introduced by median normalization in phosphoproteomics
Compensates for the bias introduced by median normalization in phosphoproteomics
CompositeDriver
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Compute coverage matrices from recount quickly using bwtool
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
Confidence estimation for intra-chromosomal contact maps
ConsensusClusterPlus
ConsensusClusterPlus
ConsensusClusterPlus
Contrasts in Mixed Effects for EMMIX Model with Random Effects
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
Copy number calling and SNV classification using targeted short read sequencing
Correct for batch effects in DNA methylation data
Correct for batch effects in DNA methylation data
Coverage visualization package for R
Coverage visualization package for R
Creates and uses physio spaces as a dimension reduction mapping
Creates diffusion maps
Creates diffusion maps
Creates diffusion maps
crisprseekplus
crisprseekplus
crisprseekplus
Decomposition of individual tumors into mutational signatures by signature refitting
derfinder helper package
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)
detect different methylation level (DMR)
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 DE genes in time series data using impulse models
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 Differentially Methylated Regions
Determining Epigenetic Heterogeneity from Bisulfite Sequencing 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 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 of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Differentially Methylated Regions caller
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.
Different test statistics based on co-citation.
DiffLogo: A comparative visualisation of biooligomer motifs
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
Earth Mover's Distance for Differential Analysis of Genomics Data
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
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
ELBOW - Evaluating foLd change By the lOgit Way
Empirical Bayes estimate of block diagonal covariance matrices
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
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
EpiMethEx Package
Epistasis Analysis for Quantitative Traits by Functional Regression Model
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
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
Exon Based Strategy for Expression Analysis of genes
Exon Based Strategy for Expression Analysis of genes
Exploration of marker-gene sequence taxonomic annotations
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 Data Analysis of LC-MS/MS data by spectral counts
Explore and download data from the recount project
Explore and download data from the recount project
Explore and download data from the recount project
Exposome exploration and outcome data analysis
Exposome exploration and outcome data analysis
Exposome exploration and outcome data analysis
Extending guilt by association by degree
Extending guilt by association by degree
Extending guilt by association by degree
Extra Base Functions for Bioconductor
Facilities for Filtering Bioconductor Annotation Resources
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
Fast Permutation-based Gene Set Analysis
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
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
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 common transcription factors in yeast expression data
Finding Mutually Exclusive Groups of Alterations in Cancer Datasets
Find SNV/Indel differences between two bam files with near relationship
Find SNV/Indel differences between two bam files with near relationship
Flexible and Customized Logo Plots using symbols, alphabets, numbers and alphanumeric strings
flexible pipelines for secretome prediction
Frozen RMA and Barcode
Frozen RMA and Barcode
Frozen RMA and Barcode
Frozen RMA Tools
Frozen RMA Tools
Frozen RMA Tools
Functional interpretation of single cell RNA-seq latent manifolds
Functional interpretation of single cell RNA-seq latent manifolds
Functions for analyzing SELEX-seq data
Functions for analyzing SELEX-seq data
Functions for annotating GRanges objects
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 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 that Apply to Rows and Columns of 'DelayedMatrix' Objects
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
Functions used to preprocess datasets stored in BioDataome
GC-SIM-MS data processing and alaysis tool
GC-SIM-MS data processing and alaysis tool
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
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 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
Generate synthetic nucleosome maps
Generating SAM file for PSMs in shotgun proteomics data
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
Gene Set Analysis in R
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
Gene Set Enrichment / Projection Displays
Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
Genome Level Trellis Layout
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
GEOsearch
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
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
GRO-seq Analysis Pipeline
GRO-seq Analysis Pipeline
GRO-seq Analysis Pipeline
GRO-seq Analysis Pipeline
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
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
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
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
High-throughput prediction of DNA shape features
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 cancer cell lines based on their weighted mutational or variational fingerprint
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
Identification of genetic Variants affecting Alternative Splicing
Identification of genetic Variants affecting Alternative Splicing
Implementation of MultiDataSet and ResultSet
Implementation of MultiDataSet and ResultSet
Implementation of MultiDataSet, ResultSet and MethylationSet
Implements the Affymetrix PLIER algorithm
Implements the Affymetrix PLIER algorithm
Imports a tRNAscan-SE result file as GRanges object
Imports a tRNAscan-SE result file as GRanges object
Imports a tRNAscan-SE result file as GRanges object
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
Inferring functionally related proteins using protein interaction networks
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 Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
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
Information Accretion-based Function Predictor Evaluation
Information Accretion-based Function Predictor Evaluation
Install/Update Bioconductor and CRAN Packages
Install/Update Bioconductor and CRAN Packages
Install/Update Bioconductor and CRAN Packages
Install/Update Bioconductor and CRAN Packages
Integration of Disease Similarity Methods
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 for Alternative Splicing
Integrative analysis of structural variations
Integrative analysis of structural variations
Integrative analysis of structural variations
Integrative network analysis of omics data
Integrative network analysis of omics data
Integrative network analysis of omics data
Interactive Differential Expression Analyzer
Interactive visualization and manipulation of nested networks
Interactive visualization and manipulation of nested networks
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
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
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
Judging Quality of Clustering Methods using Mutual Information
k-nearest neighbour batch effect test
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
LC-MS/MS Differential Expression Tests
LC-MS/MS Differential Expression Tests
LEA: an R package for Landscape and Ecological Association Studies
LEA: an R package for Landscape and Ecological Association Studies
Learning from DNA to Predict Enhancers
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
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
Linear model and normality based transformation method (Linnorm)
Linear model and normality based transformation method (Linnorm)
Linear Subpsace identification to solve complete gene expression deconvolution problem
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
Making 2D Hilbert Curve
Making 2D Hilbert Curve
Making 2D Hilbert Curve
Making 2D Hilbert Curve
Making Complex Heatmaps
Making Complex Heatmaps
Making Complex Heatmaps
Making Complex Heatmaps
Making Enriched 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
massiR: MicroArray Sample Sex Identifier
Massive and Integrative Gene Set Analysis
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
MeSH Enrichment and Semantic analyses
MeSH Enrichment and Semantic analyses
MeSH Enrichment and Semantic analyses
MeSH(Medical Subject Headings) Semantic Similarity Measures
MeSH(Medical Subject Headings) Semantic Similarity Measures
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
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
Methods for Single-Cell RNA-Seq Data Analysis
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 Spike-in Arrays
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
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
miRNAtap: microRNA Targets - Aggregated Predictions
miRNAtap: microRNA Targets - Aggregated Predictions
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
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
Multiple co-inertia analysis of omics datasets
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 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
Negative Binomial Models to detect Differential Splicing
Network Centrality Metrics for Elastic-Net Regularized Models
Network-Regularized Regression Models
Non-detects in qPCR data
Non-detects in qPCR data
Non-detects in qPCR data
Non-detects in qPCR data
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
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
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)
One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)
Online FDR control
ontology enrichment analysis
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Optimized Functional Annotation Of ChIP-seq Data
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
Outlier profile and pathway analysis in R
Package analyse 4C sequencing data
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 Topology-based Pathway Analysis of RNASeq data
Package to work with miRNAs and miRNA targets with R
Package to work with miRNAs and miRNA targets with R
PathoStat Statistical Microbiome Analysis Package
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
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
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 a maximum contrast projection of 3D images along the z-dimension into 2D
Perform methylation analysis
Perform methylation analysis
Perform methylation analysis
Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment Effect
Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment Effect
Phase template strands from Strand-seq data
Phenotype-driven module identification
Phenotype-driven module identification
Phenotyping of microbial Raman data
Phylogenetic partitioning based ILR transform for metagenomics data
Phylogenetic partitioning based ILR transform for metagenomics data
Phylogenetic partitioning based ILR transform for metagenomics data
pipeline for single cell RNA-seq data analysis
pipeline for single cell RNA-seq data analysis
PIVOT launcher
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
Plot the effect of one omics data on other omics data along the chromosome
Plotting functions for derfinder
Plotting functions for derfinder
Plotting functions for derfinder
Population-Specific Expression Analysis.
Population-Specific Expression Analysis.
Position Related Data Analysis
Position Related Data Analysis
Predict genes expressed selectively in specific cell types
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
Predicting Targets for Drosophila Intragenic miRNAs
Prediction of intronic splicing branchpoints
Prediction of intronic splicing branchpoints
Prediction of intronic splicing branchpoints
Predicts the genome build version of genomic track files
Prize: an R package for prioritization estimation based on analytic hierarchy process
Prize: an R package for prioritization estimation based on analytic hierarchy process
Probe-level Expression Change Averaging
Probe-level Expression Change Averaging
Profile score distributions
Profile score distributions
Protein co-expression network analysis (ProCoNA).
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 shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
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
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
PWM enrichment analysis
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
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
Quantify and interpret divers of variation in multilevel gene expression experiments
qusage: Quantitative Set Analysis for Gene Expression
qusage: Quantitative Set Analysis for Gene Expression
qusage: Quantitative Set Analysis for Gene Expression
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
Rank Product method for identifying differentially expressed genes with application in meta-analysis
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
R Client for Seven Bridges Genomics API (v1)
R Client for Seven Bridges Platform API
Recipes using seqsetvis
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Remove Unwanted Variation from RNA-Seq Data
Remove Unwanted Variation from RNA-Seq Data
Remove Unwanted Variation from RNA-Seq Data
Reproducibility-Optimized Test Statistic
Reproducibility-Optimized Test Statistic
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
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
R Interface to CoreArray Genomic Data Structure (GDS) Files
R Interface to CoreArray Genomic Data Structure (GDS) Files
R Interface to CoreArray Genomic Data Structure (GDS) Files
RNA Centric Annotation System
RNA Centric Annotation System
RNA Centric Annotation System
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 handling genomic interaction data
R package for handling genomic interaction data
R package for handling genomic interaction data
R package for handling genomic interaction data
R package for Manhattan Plots
R package for Manhattan Plots
R package of gene set enrichment analysis
R SDK for BaseSpace RESTful API
R SDK for BaseSpace RESTful API
R SeqAn
R Wrapper for DGIdb
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
SAFE-clustering:Single-cell Aggregated (From Ensemble) Clustering 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
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
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
Science-wise false discovery rate and proportion of true null hypotheses estimation
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
Sexual dimorphic and COPD differential analysis for gene expression and methylation.
Shiny Application for Multiplex PCR Primer Design and Analysis
Shiny Application for Multiplex PCR Primer Design and 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
Similar Binding Profiles
Similar Binding Profiles
Similarity measures for chemical compounds
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
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
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 Consensus Clustering
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single Cell Differential Expression
Single Cell Differential Expression
Single Cell Differential Expression
Single Cell Overview of Normalized Expression data
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 Targetted Network Inference
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
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
SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
Sparse Data Observations for Simulating Synthetic Abundance
Sparse Data Observations for Simulating Synthetic Abundance
Sparse Data Observations for Simulating Synthetic Abundance
SRGnet An R package for studying synergistic response genes from transcriptomics data
SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data from transcriptomics data
SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data from transcriptomics data
S-system parameter estimation method
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
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 for sparse high-throughput sequencing
Statistical Analysis of Metabolomic Data
Statistical Analysis of Metabolomic Data
Statistical Analysis of MPRA data
Statistical analysis of sequins
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 Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistical Testing for ChIP-Seq data sets
Statistical Testing for ChIP-Seq data sets
Subread sequence alignment and counting for R
Subread sequence alignment for R
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
Support for Springer monograph on Bioconductor
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
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 satistical data analysis
SWATH extended library generation and statistical data analysis
Switch-like differential expression across single-cell trajectories
Switch-like differential expression across single-cell trajectories
Switch-like differential expression across single-cell trajectories
Systems EPigenomics Inference of Regulatory Activity
Systems EPigenomics Inference of Regulatory Activity
System-wise protein turnover curve fitting
TARgeted SEQuencing Experiment Quality Control
TARgeted SEQuencing Experiment Quality Control
TARgeted SEQuencing Experiment Quality Control
Target Inhibition Interaction using Maximization and Minimization Averaging
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
Ternary Network Estimation
Test for differential expression for RNA-seq data
Test for differential expression for RNA-seq data
Testing multiple biological mediators simultaneously
Testing multiple biological mediators simultaneously
Testing multiple biological mediators simultaneously
Testing multiple biological mediators simultaneously
Test Single Package Builder
The Cancer Genome Atlas Data Integration
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
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
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 Connectivity Map-like analyses
Tools for high-throughput metabolomics
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 making reports in various formats
Tools for ordering single-cell sequencing
Tools for spliced gene structure manipulation and analysis
Tools for spliced gene structure manipulation and analysis
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 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 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 assess and compare miRNA expression estimatation methods
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
Transcription Factor High Accumulation Zones
Transcription Factor High Accumulation Zones
Transcriptomic Ovarian Cancer Datasets
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
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
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
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 self-organizing maps for visualization and interpretation of cytometry 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
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 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
Visualise microarray and RNAseq data using gene ontology annotations
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result
Visualization Tool for Sequence Recombination and Reassortment
Visualization Tool for Sequence Recombination and Reassortment
Visualizing Structure in ecological site-species abundance data
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
Workflow to process tandem MS files and build MassBank records
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
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
Zero-Inflated Negative Binomial Model for RNA-Seq Data