Biocview "Software"

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
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 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.
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 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 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 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 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
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.
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 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 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
A search tool for single cell RNA-seq data by gene lists
A Shiny App to accompany clusterExperiment
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 SummarizedExperiment for Ivy-GAP data
Asymptotic tests and model fitting for extreme phenotype sampling
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
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
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
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
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 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
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 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 genomic data
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
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
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
Classification of RNA-seq data from ALL samples
Classification of RNA-seq data from ALL samples
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
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
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
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
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
ConsensusClusterPlus
ConsensusClusterPlus
ConsensusClusterPlus
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 diffusion maps
Creates diffusion maps
Creates diffusion maps
crisprseekplus
crisprseekplus
crisprseekplus
derfinder helper package
derfinder helper package
derfinder helper package
detect different methylation level (DMR)
detect different methylation level (DMR)
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
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
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 sequence 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
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
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
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
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
Factor Loading Adaptive SHrinkage in R
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
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 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 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 similarities
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 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
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 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 / 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
Genomic Knowledge-guided Multiple Testing
GEOsearch
GEOsearch
GEOsearch
Get the QTL/gene/SNP data functions
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 in R
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
Helper functions for creating a MultiAssayExperiment instance with TCGA data
Helper functions for creating a MultiAssayExperiment instance with TCGA data
Helper functions for creating a MultiAssayExperiment instance with TCGA data
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 of cancer cell lines based on their weighted mutational or variational fingerprint
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 genetic Variants affecting Alternative Splicing
Identification of genetic Variants affecting Alternative Splicing
Implementation of MultiDataSet and ResultSet
Implementation of MultiDataSet, ResultSet and MethylationSet
Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and MethylationSet
Implements the Affymetrix PLIER algorithm
Implements the Affymetrix PLIER algorithm
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 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
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
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 of Fluorescence Dilution Experiments
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
Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics
Joint Segmentation of Multivariate (Copy Number) Signals
Joint Segmentation of Multivariate (Copy Number) Signals
Joint Segmentation of Multivariate (Copy Number) Signals
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, Pathway and Network 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)
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
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
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
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 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
Network-Regularized Regression Models
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
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)
ontology enrichment analysis
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 EDLogo visualization, featuring string logos and adaptive scaling of position weight matrices
Package for Topology-based Pathway Analysis of RNASeq data
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
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
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
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
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
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
qusage: Quantitative Set Analysis for Gene Expression
qusage: Quantitative Set Analysis for Gene Expression
qusage: Quantitative Set Analysis for Gene Expression
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
R Client for Seven Bridges Genomics API (v1)
R Client for Seven Bridges Platform API
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
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
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 Manhattan Plots
R package for Manhattan Plots
R SDK for BaseSpace RESTful API
R SDK for BaseSpace RESTful API
R Wrapper for DGIdb
R Wrapper for DGIdb
R Wrapper for DGIdb
R wrapper for the OMA REST API
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
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP 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
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
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-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
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 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 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 satistical 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
System-wise protein turnover curve fitting
TARgeted SEQuencing Experiment Quality Control
TARgeted SEQuencing Experiment Quality Control
Target Inhibition Interaction using Maximization and Minimization Averaging
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
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
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 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
Transcriptional analysis based on transcriptograms
Transcription Factor High Accumulation Zones
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
Two dimensional visualization of single-cell 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
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 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
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 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