All R packages

Found 1321 packages.

Automated Affymetrix Array Analysis Umbrella Package
Automated Affymetrix Array Analysis Base Package
Automated Affymetrix Array Analysis Classification Package
Automated Affymetrix Array Analysis Core Package
Automated Affymetrix Array Analysis Preprocessing Package
Automated Affymetrix Array Analysis Reporting Package
Gene expression enrichment in human brain regions
Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
Artificial Components Detection of Differentially Expressed Genes
Classes and functions for Array Comparative Genomic Hybridization data.
Algorithms for Calculating Microarray Enrichment (ACME)
Analysis of big data from aCGH experiments using parallel computing and ff objects
Annotation-Driven Clustering
Affymetrix File Parsing SDK
Methods for Affymetrix Oligonucleotide Arrays
Graphics Toolbox for Assessment of Affymetrix Expression Measures
Affymetrix GeneChip software compatibility
structured corruption of affymetrix cel file data
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
Affymetrix Quality Assessment and Analysis Tool
Linear Model of background subtraction and the Langmuir isotherm
Tools for parsing Affymetrix data files
GUI for limma package with Affymetrix microarrays
Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays
Probe Dependent Nearest Neighbours (PDNN) for the affy package
Methods for fitting probe-level models
QC Report Generation for affyBatch objects
Analyze and correct probe positional bias in microarray data due to RNA degradation
Easy extraction of individual probes in Affymetrix tiling arrays
Agreement of Differential Expression Analysis
Agilent expression array processing package
Processing and Differential Expression Analysis of Agilent microRNA chips
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
Analysis Of Differential Abundance Taking Sample Variation Into Account
Investigates Allele Specific Expression
alpine
ALS for the Automatic Chemical Exploration of mixtures
alternative CDF environments (aka probeset mappings)
Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
Analysis of amplicon enrichment panels
A framework for sharing interactive data and plots from R through the web.
An integrated analysis package of miRNA and mRNA expression data
Statistical analysis of sequins
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Annotation tools for Affymetrix biological metadata
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
Annotation for microarrays
Annotation Database Interface
Code for Building Annotation Database Packages
Annotation translation functions
Client to access AnnotationHub resources
Transform public data resources into Bioconductor Data Structures
Annotate microarrays and perform cross-species gene expression analyses using flat file databases.
Annotation of Genomic Regions to Genomic Annotations
ANalysis Of Translational Activity (ANOTA).
Implementation of gene expression anti-profiles
Estimate protein complex membership using AP-MS protein data
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
ArrayExpress High Throughput Sequencing Processing Pipeline
multivariate outlier detection for expression array QA
Assessing array quality on spotted arrays
Quality metrics report for microarray data sets
geneChip Analysis Package
Implementation of wave correction for arrays
Adaptive Robust Regression normalization for Illumina methylation data
Ancestry Specific Allele Frequency Estimation
Predict Acetylated Lysine Sites
Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models
All sample mean normalization.
Analysis of alternative splicing using RNA-Seq
An R package for subset-based association analysis of heterogeneous traits and subtypes
Adaptive Signature Selection and InteGratioN (ASSIGN)
Gene Expression Atlas query and gene set enrichment package.
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Bayesian Analysis of Chip-chip experiment
Controlling bias and inflation in association studies using the empirical null distribution
Bayesian Analysis of Differential Expression in RNA Sequencing Data
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
A Bayesian Approach for Geneset Selection
Flexible, isoform-level differential expression analysis
Extract read count signals from bam files
R SDK for BaseSpace RESTful API
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Basic peak calling on STARR-seq data
Batch Effects Quality Control Software
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
Bayesian Analysis of ChIP-seq Data
Empirical Bayesian analysis of patterns of differential expression in count data
BBCAnalyzer: an R/Bioconductor package for visualizing base counts
Predicting binding site consensus from ranked DNA sequences
Quality assessment and low-level analysis for Illumina BeadArray data
Normalization and reporting of Illumina SNP bead arrays
Compression of Illumina BeadArray data
BEAT - BS-Seq Epimutation Analysis Toolkit
Correct for batch effects in DNA methylation data
Identify differentially expressed genes in microarray time-course data
BGAfun A method to identify specifity determining residues in protein families
Annotation and gene expression data retrieval from Bgee database
Bayesian models for differential gene expression
Bayesian Gene eXpression
Bayesian Hierarchical Clustering
Biclustering Analysis and Results Exploration
Constraint based modeling in R using metabolic reconstruction databases
Illumina methylation array analysis for large experiments
An extension of the bigmemory package with added safety, convenience, and a factor class
Cross-target analysis of small molecule bioactivity
Biobase: Base functions for Bioconductor
Turn Bioconductor objects into tidy data frames
Interactive Multi-Omics Cancers Data Visualization and Analysis
BiocCaseStudies: Support for the Case Studies Monograph
Bioconductor-specific package checks
S4 generic functions for Bioconductor
Graph examples and use cases in Bioinformatics
Install/Update Bioconductor, CRAN, and github Packages
Bioconductor facilities for parallel evaluation
Standard styles for vignettes and other Bioconductor documents
Categorized views of R package repositories
Tools to aid the development of Bioconductor Workflow packages
Different distance measures
Interface to BioMart databases (e.g. Ensembl, COSMIC, Wormbase and Gramene)
An interface package for the BIOM file format
Model-View-Controller (MVC) Classes That Use Biobase
Copy Number study and Segmentation for multivariate biological data
Routines for the functional analysis of biological networks
Detect tissue heterogeneity in expression profiles with gene sets
Classification for Biological Sequences
Signature discovery from omics data
String objects representing biological sequences, and matching algorithms
Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling
Basic graphic utilities for visualization of genomic data.
High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)
Bayesian Inference of Regulation of Transcriptional Activity
Bayesian Inference of Regulatory Influence on Expression (biRte)
Processing and analyzing bisulfite sequencing data
Transcript expression inference and differential expression analysis for RNA-seq data
Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.
Model higher-order methylation profiles
Baffling Recursive Algorithm for Isotope distributioN calculations
query gene expression data and plots from BrainStars (B*)
Bayesian Robust Inference for Differential Gene Expression
Code for using BridgeDb identifier mapping framework from within R
BrowserViz: interactive R/browser graphics using websockets and JSON
BrowserVizDemo: How to subclass BrowserViz
Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation
Analyze, manage and store bisulfite sequencing data
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
A matrix data storage object held in temporary files
Microarray Data related methods that utlize BufferedMatrix objects
Bump Hunter
Gene network reconstruction
Chromosmal Aberrations Finder in Expression data
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Calibration model for estimating absolute expression levels from microarray data
Collection of annotation related methods for mass spectrometry data
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC.
Development and validation of diagnostic tests from high-dimensional molecular data
An R interface for computational modeling of tumor progression
Cancer mutation analysis
Cancer subtypes identification, validation and visualization based on genomic data
Perform Chromosomal Ancestry Differences (CAnD) Analyses
Visualization of multi-dimentional cancer genomics data
A mass spectrometry imaging toolbox for statistical analysis
Characterization of Alternative Splicing based on Paired-End Reads
Category Analysis
Meta-analysis of high-throughput experiments using feature annotations
Causal Reasoning Methods
Combination Connectivity Mapping
PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data
ccrepe_and_nc.score
Fitting cell population growth models
Analysis of cell-based screens
Analysis of cell-based screens - revised version of cellHTS
Quality Control for Single-Cell RNA-seq Data
Predict genes expressed selectively in specific cell types
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
Statistical analysis for the Colony Formation Assay
An R package for analysis of case-control studies in genetic epidemiology
CGHbase: Base functions and classes for arrayCGH data analysis.
Calling aberrations for array CGH tumor profiles.
Find chromosome regions showing common gains/losses
Normalization of array CGH data with imbalanced aberrations.
Dimension Reduction for Array CGH Data with Minimal Information Loss.
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Analysis of DNA methylation data from CHARM microarrays
R interface to a subset of OpenBabel functionalities
Cheminformatics Toolkit for R
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
A package for secondary analysis of fusion products
Quantitative comparison of multiple ChIP-seq datasets
Gene Set Enrichment For ChIP-seq Peak Data
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
Quality metrics for ChIPseq data
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
chipseq: A package for analyzing chipseq data
Identifying Protein Binding Sites in High-Throughput Sequencing Data
Simulation of ChIP-seq experiments
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
The snp.matrix and X.snp.matrix classes
chroGPS: visualizing the epigenome
chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.
Heat map plotting by genome coordinate
Global visualization tool of genomic data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
Chromosome Instability Index
Visualization and management of the protein-protein interaction networks.
A framework for two-class classification problems, with applications to differential variability and differential distribution testing
This package classifies putative polyadenylation sites as true or false/internally oligodT primed
Cleavage of Polypeptide Sequences
A package for the clinical proteomic profiling data analysis
Gene Set Analysis Exploiting Pathway Topology
Infers clonal composition of a tumor
Clonality testing
High throughput analysis of T cell antigen receptor sequences
Classification by local similarity threshold
Tools for performing taxonomic assignment.
Clustering Comparison Package
Compare clusterings for single-cell sequencing
statistical analysis and visualization of functional profiles for genes and gene clusters
The ClusterSignificance package provides tools to assess if clusters have a separation different from random or permuted data
Compute cluster stability scores for microarray data
Synthesis of microarray-based classification
A normalization method for Copy Number Aberration in cancer samples
CNE Detection and Visualization
cn.FARMS - factor analysis for copy number estimation
cn.mops - Mixture of Poissons for CNV detection in NGS data
Add-on to CellNOptR: Discretized time treatments
Integration of CellNOptR to add missing links
Addon to CellNOptR: Fuzzy Logic
ODE add-on to CellNOptR
Bayesian mixture models for copy number polymorphisms
Convert segment data into a region by sample matrix to allow for other high level computational analyses.
Gene Set Analysis of (Rare) Copy Number Variants
Reliable CNV detection in targeted sequencing applications
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
A package to test genetic association with CNV data
Finding Co-occuring motifs of transcription factor binding sites
Different test statistics based on co-citation.
Manipulation of Codelink microarray data
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
Coordinated Gene Activity in Pattern Sets
co-expressed gene-set enrichment analysis
cancer outlier Gene Profile Sets
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
Combinatorial Polyfunctionality Analysis of Single Cells
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
Tools for computational epigenomics
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
Making Complex Heatmaps
Cell OrderiNg by FluorEScence Signal
ConsensusClusterPlus
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Improves Early Build Genome Assemblies using Strand-Seq Data
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Convert Microarray Data Objects
Functions to perform cancer outlier profile analysis.
Sexual dimorphic and COPD differential analysis for gene expression and methylation.
Segmentation of single- and multi-track copy number data by penalized least squares regression.
R package for calling CNV from Illumina 450k methylation microarrays
Copy number information from targeted sequencing using off-target reads
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
Correlation Motif Fit
Detect the correlated mutations based on selection pressure
Analysis of co-knock-down RNAi data
Multivariate Correlation Estimator and Statistical Inference Procedures.
cosmiq - COmbining Single Masses Into Quantities
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Empirical Bayes estimate of block diagonal covariance matrices
Coverage visualization package for R
Multivariate Analysis of Transcriptomic Data
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Conditional quantile normalization
CRImage a package to classify cells and calculate tumour cellularity
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
crisprseekplus
Tools for counting and visualising mutations in a target location
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Cross Platform Meta-Analysis of Microarray Data
Statistical tools for the analysis of ChIP-seq data
ChIP-Seq Analysis with Windows
ChIP-Seq Statistical Power
Cluster and Tree Conversion.
Clustering of Time Series Gene Expression data
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search.
Cancer Variant Explorer
Significance of periodic expression pattern in time-series data
cytofkit: an integrated mass cytometry data analysis pipeline
GatingML interface for openCyto
Accurate, high-resolution sample inference from amplicon sequencing data
dagLogo
Efficient design and analysis of factorial two-colour microarray data
Tools for the Differential Analysis of Proteins Abundance with R
Denoising Algorithm based on Relevance network Topology
Distributed Annotation System in R
Retrieval from the DAVID bioinformatics data resource into R
Differential Binding of Transcription Factor with ChIP-seq
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
Distinguish direct and indirect interactions with Graphical Modelling
debrowser: Interactive Differential Expresion Analysis Browser
Tools for curating, analyzing, and manipulating biological sequences
Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
Differential Expression via Distance Summary for Microarray Data
DeepBlueR
Detection of subclonal SNVs in deep sequencing data.
Differential gene expression data formats converter
Two-sample tests on a graph
Report of DEG analysis
Identify Differentially Expressed Genes from RNA-seq data
deltaGseg
DeMAND
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
derfinder helper package
Plotting functions for derfinder
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Creates diffusion maps
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
Inference of differential exon usage in RNA-Seq
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
Gene Selection
Differential Binding Analysis of ChIP-Seq peak data
Performs differential gene expression Analysis
Differential Analyis of Hi-C Data
DiffLogo: A comparative visualisation of sequence motifs
Identifying differential DNA loops from chromatin topology data
Inference of Genetic Variants Driving Cellular Phenotypes
A dynamic visualization tool of multi-level data
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
Differentially Methylated Regions caller
Methylation array and sequencing spatial analysis methods
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
DNA copy number data analysis
DNase I footprinting analysis of DNase-seq data
High-throughput prediction of DNA shape features
Geneset enrichment based on InterPro domain signatures
Identify likely duplicate samples from genomic or meta-data
Genotyping and QTL Mapping in DO Mice
Disease Ontology Semantic and Enrichment analysis
Differential splicing and sQTL analyses with Dirichlet-multinomial model in RNA-Seq
Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer
Comparison of disease and drug profiles using Gene set Enrichment Analysis
Integration of Disease Similarity Methods
Dispersion shrinakge for sequencing data.
Dynamic Transcriptome Analysis
Dual KS Discriminant Analysis and Classification
a package for checking high-throughput genomic data redundancy in meta-analysis
Assessment of duplication rates in RNA-Seq datasets
The GASSCO method for correcting for slide-dependent gene-specific dye bias
Dynamic document tools
EasyqpcR for low-throughput real-time quantitative PCR data analysis
Count summarization and normalization for RNA-Seq data
Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
EBcoexpress for Differential Co-Expression Analysis
Image processing and analysis toolbox for R
Exon Based Strategy for Expression Analysis of genes
An R package for gene and isoform differential expression analysis of RNA-seq data
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Meta-data and tools for E. coli
Exploratory Data Analysis and Normalization for RNA-Seq
Experimental Design in Differential Abundance analysis
Extraction of Differential Gene Expression
Empirical Analysis of Digital Gene Expression Data in R
Engineering Evaluation by Gene Categorization (eegc)
Extending guilt by association by degree
Ensemble of Gene Set Enrichment Analyses
Accelerated similarity searching of small molecules
Expression data analysis via the Iterative Signature Algorithm
ELBOW - Evaluating foLd change By the lOgit Way
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Earth Mover's Distance for Differential Analysis of Genomics Data
Uses Brown's method to combine p-values from dependent tests
A compilation of ENCODE metadata
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Making Enriched Heatmaps
Seamless navigation through combined results of set-based and network-based enrichment analysis
Utilities to create and use an Ensembl based annotation database
R Interface to Ensembl Variant Effect Predictor
Retrieval from the ENVISION bioinformatics data portal into R
Epigenetic and gene transcription data normalization and integration with mixture models
R Interface to epiviz web app
Data Management API for epiviz interactive visualization app
WebSocket server infrastructure for epivizr apps and packages
Run Epiviz Interactive Genomic Data Visualization App within R
Assess Differential Gene Expression Experiments with ERCC Controls
epigenomic road map adventures
Visualizations of expressionSet Bioconductor object
Cartesian plot and contingency test on 16S Microbial data
Expression Weighted Celltype Enrichment
R functions for the normalization of Exiqon miRNA array data
Copy number variant detection from exome sequencing read depth
exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis
Client to access ExperimentHub resources
Add resources to ExperimentHub
GUI for exploratory data analysis of systems biology data
Download datasets from EMBL-EBI Expression Atlas
Visualize biclusters identified in gene expression data
FABIA: Factor Analysis for Bicluster Acquisition
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Factorial designed microarray experiment analysis
Pedigree Analysis and Familial Aggregation
FARMS - Factor Analysis for Robust Microarray Summarization
functions for genome-wide application of Liquid Association
fastseg - a fast segmentation algorithm
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics
FDR adjustments of Microarray Experiments (FDR-AME)
Identification of Functional Epigenetic Modules
Quality assessment and control for FFPE microarray expression data
Functional Gene Networks derived from biological enrichment analyses
Fast Gene Set Enrichment Analysis
Microbial Comparative Genomics in R
FISHalyseR a package for automated FISH quantification
Confidence estimation for intra-chromosomal contact maps
Analysis of Metabolomics GC/MS Data
Fast lasso-based isoform prediction as a flow problem
Automatic and interactive quality control for flow cytometry data
flowBeads: Analysis of flow bead data
Combining multitube flow cytometry data by binning
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
Analyze flow cytometric data using histogram information
Semantic labelling of flow cytometric cell populations
flowClean
Clustering for Flow Cytometry
flowCore: Basic structures for flow cytometry data
Analyze flow cytometric data using gate information
Sequential Flow Cytometry Data Gating
Estimate proliferation in cell-tracking dye studies
Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm.
Fingerprinting for Flow Cytometry
Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test
Matching and meta-clustering in flow cytometry
Non-parametric Flow Cytometry Data Gating
Cluster Merging for Flow Cytometry Data
An R package for flow data clustering
Methods for Continuous Flow Cytometry
Analyze flow cytometer data to determine sample ploidy
flowPlots: analysis plots and data class for gated flow cytometry data
Quality control for flow cytometry
Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations
FlowRepository R Interface
Using self-organizing maps for visualization and interpretation of cytometry data
Statistical methods for the analysis of flow cytometry data
Parameter Optimization for Flow Cytometry Data Transformation
Phenotyping Flow Cytometry Assays
Utilities for flow cytometry
Visualization for flow cytometry
Variance stabilization in flow cytometry (and microarrays)
Infrastructure for representing and interacting with the gated cytometry
Mismatch Tolerant Maximum Common Substructure Searching
Detection of focal aberrations in DNA copy number data
Package analyse 4C sequencing data
Epistasis Analysis for Quantitative Traits by Functional Regression Model
Frozen RMA and Barcode
Frozen RMA Tools
Clustering and Alignment of ChIP-Seq peaks based on their shapes
Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
GaGa hierarchical model for high-throughput data analysis
Generally Applicable Gene-set Enrichment for Pathway Analysis
Broadcast data between R and Gaggle
GAIA: An R package for genomic analysis of significant chromosomal aberrations.
Prediction of gestational age with Illumina HumanMethylation450 data
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
Genotype Conditional Association TEST
Tools for Connectivity Map-like analyses
A web interface for gene-set enrichment analyses
Suite of Functions for Pooled Crispr Screen QC and Analysis
Background Adjustment Using Sequence Information
R Interface to CoreArray Genomic Data Structure (GDS) Files
Gene Set Enrichment Analysis Extended to Contingency Cubes
GEM: fast association study for the interplay of Gene, Environment and Methylation
Microarray Analysis tool
Parsing GenBank files into semantically useful objects
Integrated Interpretation of Genes
Identification of candidate genes associated with genetic variation
Gene Break Detection
Interact with GENE-E from R
Gene Expression Signature based Similarity Metric
genefilter: methods for filtering genes from high-throughput experiments
Computation of Gene Expression-Based Signatures in Breast Cancer
Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
Tools for Testing Gene-Gene Interaction at the Gene Level
MetaAnalysis for High Throughput Experiments
Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
Test and visualize gene overlaps
Evolutionary and plasticity analysis based on orthologous groups distribution
Graphics related functions for Bioconductor
A gene recommender algorithm to identify genes coexpressed with a query set of genes
GeneRegionScan
gRx Differential Clustering
Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions
Stability and Aggregation of ranked gene lists
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Classify diseases and build associated gene networks using gene expression profiles
Functions for designing genetics studies
Pedigree and genetic relationship functions
Optimal Gene Extensions From Histone Modification ChIP-seq Data
genotyping and copy number study tools
A GAM based framework for analysis of ChIP-Seq data
Summary, annotation and visualization of genomic data
Plotting genomic information from Ensembl
Utilities for manipulating chromosome and other 'seqname' identifiers
Operations on genomic intervals
Genome sequencing project metadata
Representation and manipulation of short genomic alignments
Tools for making and manipulating transcript centric annotations
Distributed computing by file or by range
R package for handling genomic interaction data
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and Manipulation of Genomic Tuples
Analyze, manage and store genomic data
A RangedSummarizedExperiment with methods for copy number analysis
QA/QC of a gVCF or VCF file
A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models
Candidate gene prioritization based on convergent evidence
Genomic Visualizations in R
A compilation of metadata from NCBI GEO
Get data from NCBI Gene Expression Omnibus (GEO)
GEOsearch
Prepares microarray data for submission to GEO
Gene-Specific Phenotype EstimatoR
Gene Environment Wide Interaction Search Threshold
GGBase infrastructure for genetics of gene expression package GGtools
Visualization tools for genomic data.
Visualize Cytometry data with ggplot
software and data for analyses in genetics of gene expression
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
Genome Intervals and Read Alignments for Functional Exploration
Gain and Loss Analysis of DNA
Interactive HTML graphics
Calculates a global test for differential gene expression between groups
Testing for association between RNA-Seq and high-dimensional data
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
An R interface to the GMAP/GSNAP/GSTRUCT suite
GWAS-based Mendelian Randomization and Path Analyses
Visualise microarray and RNAseq data using gene ontology annotations
GO-function: deriving biologcially relevant functions from statistically significant functions
R Client for Google Genomics API
Find the most characteristic gene ontology terms for groups of human genes
goProfiles: an R package for the statistical analysis of functional profiles
GO-terms Semantic Similarity Measures
Gene Ontology analyser for RNA-seq and other length biased data
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Tools for manipulating GO and microarrays.
Word cloud summaries of GO enrichment analysis
Binomial test for Hi-C data analysis
Functions for Gene Ontology database
Classification using generalized partial least squares
Gaussian Process Ranking and Estimation of Gene Expression time-series
gQTLBase: infrastructure for eQTL, mQTL and similar studies
gQTLstats: computationally efficient analysis for eQTL and allied studies
graph: A package to handle graph data structures
GraphAlignment
Graph Theoretic Association Tests
GRAPH Interaction from pathway Topological Environment
Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.
Gene Regulatory Network Inference Using Time Series
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
Calculate growth-rate inhibition (GR) metrics
GRO-seq Analysis Pipeline
Fast Permutation-based Gene Set Analysis
Gene Set Analysis in R
GSCA: Gene Set Context Analysis
Gene set enrichment data structures and methods
Linear Model Toolset for Gene Set Enrichment Analysis
Gene Set Regulation (GS-Reg)
Gene Set Regulation Index
Gene Set Variation Analysis for microarray and RNA-seq data
Genome Level Trellis Layout
GUIDE-seq analysis pipeline
Guitar
Plotting data and annotation information along genomic coordinates
representing and modeling data in the EMBL-EBI GWAS catalog
Tools for Genome Wide Association Studies
Managing alignment tallies using a hdf5 backend
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
A "corrective make-up" program for microarray chips
Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
An array-like container for convenient access and manipulation of HDF5 datasets
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Heatmaps with row and/or column covariates and colored clusters
Introduce *Ranges to bedtools users
Tools for HELP data analysis
Heterogeneous error model for identification of differentially expressed genes under multiple conditions
Functions for annotating GRanges objects
HLA Genotype Imputation with Attribute Bagging
Asessing statistical significance in predictive GWA studies
Making 2D Hilbert Curve
Hilbert curve visualization
HilbertVisGUI
Functions to process LM-PCR reads from 454/Illumina data
High Throughput Chromosome Conformation Capture analysis
Copy number prediction with correction for GC and mappability bias for HTS data
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Human Protein Atlas in R
Automated analysis of high-throughput qPCR data
Gene set over-representation, enrichment and network analyses for high-throughput screens
A NGS analysis pipeline.
Quality Control, Visualization and Processing for High-Throughput Sequencing data
Filter replicated high-throughput transcriptome sequencing data
Hybrid Multiple Testing
Visualizing Hypergaphs
A package providing hypergraph data structures
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
Iterative Binary Biclustering of Genesets
Interaction Based Homogeneity for Evaluating Gene Lists
integrated Bayesian Modeling of eQTL data
A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)
NPMLE for Censored and Truncated Data
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
Integrative clustering of multi-type genomic data
Comparison and Visualization of Ranking and Assignment Methods
Plots data (continuous/discrete) along chromosomal ideogram
idiogram
ID Mapping Analysis
ID Mapping Data Retrieval
An integrated analysis package of Gene expression and Copy number alteration
Independent Hypothesis Weighting
Parsing Illumina Microarray Output Files
Analysis of high-throughput microscopy-based screens
A graphical interface for the metagene package
A Thin Wrapper around the ImmuneSpace Database
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
Retrieves data from IMPC database
Detection of DE genes in time series data using impulse models
impute: Imputation for microarray data
Identification of Novel alternative PolyAdenylation Sites (PAS)
An R package for computing the number of susceptibility SNPs
Access to the InSilico Database
Collection of Merging Techniques for Gene Expression Data
Analysis of 4sU-seq and RNA-seq time-course data
Integrative analysis of structural variations
Base Classes for Storing Genomic Interaction Data
Package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Inversions in genotype data
Quality Assessment Tools for Oxford Nanopore MinION data
Data management and analysis of ion trees from ion-trap mass spectrometry
Identification of Protein Amino acid Clustering
Automated Optimization of XCMS Data Processing parameters
Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching
Infrastructure for manipulating intervals on sequences
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
Analysis and quantitation of isobarically tagged MSMS proteomics data
A graphical user interface to conduct a dose-response analysis of microarray data
Integrative Statistics of alleLe Dependent Expression
Analyze isomiRs and miRNAs from small RNA-seq
ITALICS
The Iterative Bayesian Model Averaging (BMA) algorithm
The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
Identification of genetic Variants affecting Alternative Splicing
Joint analysis of multiple ChIP-Seq data sets
JODA algorithm for quantifying gene deregulation using knowledge
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
Multi sample aCGH analysis package using kernel convolution
Kernel-Based Analysis Of Biological Sequences
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
graph support for KO, KEGG Orthology
An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway
Client-side REST access to KEGG
A k-tables approach to integrate multiple Omics-Data
Laplace Mixture Model in Microarray Experiments
Estimation of the false discovery rate.
data structures for linkage disequilibrium measures in populations
LEA: an R package for Landscape and Ecological Association Studies
Learning from DNA to Predict Enhancers
Identifying Differential Effects in Tiling Microarray Data
Logistic Factor Analysis for Categorical Data
Linear Models for Microarray Data
GUI for limma package with two color microarrays
co-expression of lincRNAs and protein-coding genes
Linear model and normality based transformation method (Linnorm)
LiquidAssociation
Linear Model decomposition for Designed Multivariate Experiments
LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Identification of SNP Interactions
logit-t Package
Lots Of Lasso
Location overlap analysis for enrichment of genomic ranges
LowMACA - Low frequency Mutation Analysis via Consensus Alignment
Methods for analyzing microarray data using Local Pooled Error (LPE) method
A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.
Linear Programming Model for Network Inference
Symphony integer linear programming solver in R
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
LVS normalization for Agilent miRNA data
Analyze high-throughput sequencing of T and B cell receptors
Identifies differentially methylated regions across testing groups
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Tools for analyzing Micro Array experiments
MicroArray Chromosome Analysis Tool
Visualize artificial correlation in microarray data
Multivariate analysis of microarray data using ADE4
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
Summarize, Analyze and Visualize MAF files
Functions to handle cDNA microarray data, including several methods of data analysis
Statistical Analysis of Metabolomic Data
CDF Environment Maker
CGH Micro-Array NORmalization
Microbial Assemblage Normalized Transcript Analysis
Compute Mantel Cluster Correlations
A Hybrid Feature Selection method for gene expression data
Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge
Exploratory analysis for two-color spotted microarray data
Significant Gene Expression Profile Differences in Time Course Gene Expression Data
Masking probes with binding affinity differences
Analytical Tools for MassArray Data
massiR: MicroArray Sample Sex Identifier
Mass spectrum processing by wavelet-based algorithms
Model-based Analysis of Single Cell Transcriptomics
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.
Obtain total affinity and occupancies for binding site matrices on a given sequence
A framework for rapid prototyping with binary data on disk
Model-based analysis of DNA methylation data
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
MBCB (Model-based Background Correction for Beadarray)
Bayesian Piecewise Constant Regression for DNA copy number estimation
Multiple Beta t-Tests
Microbial Community Analysis GUI
Misclassification error estimation with cross-validation
Multi Dimensional Gene Set Analysis.
Mahalanobis Distance Quality Control for microarrays
Perform methylation analysis
Measurement Error model estimate for correlation coefficient
DNA IP-seq data analysis
Modelling Experimental Data from MeDIP Enrichment
MEIGO - MEtaheuristics for bIoinformatics Global Optimization
Merge Maid
Integrative network analysis of omics data
DBI to construct MeSH-related package from sqlite file
MeSH Enrichment and Semantic analyses
Tools for conducting enrichment analysis of MeSH
MeSH(Medical Subject Headings) Semantic Similarity Measures
Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems.
Integration of Microarray Data for Meta-analysis
Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
A package to run mixture models for truncated metabolomics data with normal or lognormal distributions
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
A package to produce metagene plots
Exploration of marker-gene sequence taxonomic annotations
Statistical analysis for sparse high-throughput sequencing
Hierarchical Dependence in Meta-Analysis
MS-based metabolomics annotation pipeline
Meta-analysis of RNA-Seq count data in multiple studies
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for metabolomic data analysis
A workflow to analyse and visualise metabolomics data
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
Perform Methylation Analysis on Next Generation Sequencing Data
Methods for visualization and statistics on DNA methylation data
DNA methylation data analysis and visualization
Visual and interactive quality control of large Illumina DNA Methylation array data sets
DNA methylation analysis from high-throughput bisulfite sequencing results
MethylMix: Identifying methylation driven cancer genes
detect different methylation level (DMR)
Base resolution DNA methylation data analysis
Segmentation of Bis-seq data
Handle Illumina methylation data
Soft clustering of time series gene expression data
Marker Gene Finder in Microarray gene expression data
Marker Gene Finder in RNA-seq data
Model-based gene set analysis
MiChip Parsing and Summarizing Functions
Data and functions for dealing with microRNAs
Mixture Models for Single-Cell Assays
Analysis of an ICA decomposition obtained on genomics data
Mutual Information NETworks
Analyze Illumina Infinium DNA methylation arrays
A Package for De Novo CNV Detection in Case-Parent Trios
Misclassification Penalized Posterior Classification
MiRNA Ranking by Gene Expression
Tools to assess and compare miRNA expression estimatation methods
Integrating microRNA expression into signaling pathways for pathway analysis
Dry lab for exploring miRNA-mRNA relationships
Convert miRNA Names to Different miRBase Versions
miRNApath: Pathway Enrichment for miRNA Expression Data
miRNAtap: microRNA Targets - Aggregated Predictions
Mirsynergy
Analysing Illumina HumanMethylation BeadChip Data
Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"
Uniform interfaces to R machine learning procedures for data in Bioconductor containers
MLP
Machine learning interface for RNA-Seq data
Statistical Testing for ChIP-Seq data sets
Statistical Testing for ChIP-Seq data sets
A metagenomic pipeline for systems biology
Murine Palate miRNA Expression Analysis
MODA: MOdule Differential Analysis for weighted gene co-expression network
Multiple omics data integrative clustering and gene set analysis
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Identify oncogenes and tumor suppressor genes from omics data
MoPS - Model-based Periodicity Screening
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
An Annotated Collection of Protein-DNA Binding Sequence Motifs
A package for discriminative motif discovery, designed for high throughput sequencing dataset
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Motif Identification and Validation
Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data
Metabolomic Quantitative Trait Locus Mapping for 1H NMR data
Multiple Sequence Alignment
A shiny GUI for MSGFplus
An interface between R and MS-GF+
Exploratory Data Analysis of LC-MS/MS data by spectral counts
LC-MS/MS Differential Expression Tests
Base Functions and Classes for MS-based Proteomics
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Calculates Mulcom test
Create Classes and Functions for Managing Multiple Assays on Sets of Samples
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and MethylationSet
Testing multiple biological mediators simultaneously
R package for combining multiple scans
Resampling-based multiple hypothesis testing
Multiple Sequence Alignment with MUSCLE
Studying patterns in base substitution catalogues
Model-View-Controller (MVC) Classes
Multivariate and directional gene set testing
Access MyGene.Info_ services
Accesses MyVariant.info variant query and annotation services
An mzIdentML parser for R
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
Differential Expression Analysis of NanoString nCounter Data
Quality metrics and data processing methods for NanoString mRNA gene expression data
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
Pathways from the NCI Pathways Database
An R package to perform the network enrichment analysis (NEA).
(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
Benchmarking of several gene network inference methods
A package for visualizing complex biological network
A bioconductor package for high-dimensional exploration of biological network heterogeneity
NetPathMiner for Biological Network Construction, Path Mining and Visualization
A model for network-based prioritisation of genes
Functional Network Analysis
Network Seriation And Modularization
Regression-based network inference using Bayesian Model Averaging
NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing
Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
Exploratory analysis and differential expression for RNA-seq data
Non-detects in qPCR data
Preprocessing of Illumina Infinium 450K data
Functions for normalisation of RT-qPCR data
Normalization and difference calling in ChIP-seq data
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Predict gene network using an Ordinary Differential Equation (ODE) based method
Generate synthetic nucleosome maps
Nucleosome positioning package for R
Normal Uniform Differential Gene Expression detection
An R package for nucleosome positioning prediction
Functions for Multinomial Occupancy Distribution
Operating characteristics plus sample size and local fdr for microarray experiments
Outlier detection in multiple sequence alignments
Outlier Gene Set Analysis
Preprocessing tools for oligonucleotide arrays
Classes for high-throughput arrays supported by oligo and crlmm
Optimized local intensity-dependent normalisation of two-color microarrays
Graphical user interface for OLIN
Multiple co-inertia analysis of omics datasets
High-quality circular visualization of omics data
Classification and Feature Selection for 'Omics' Datasets
A tool to identify potentially oncogenic genes
Forward Genetic Simulation of Cancer Progression with Epistasis
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
Ontology traversal and search
Hierarchical Gating Pipeline for flow cytometry data
An R package of Data Importing, Processing and Analysis for Opera High Content Screening System
Comprehensive analysis of transciptome data
Outlier profile and pathway analysis in R
Similarities of Ordered Gene Lists
Software to enable the smooth interfacing of different database packages
OSAT: Optimal Sample Assignment Tool
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Provides structure and functions for the analysis of OTU data
Outlier detection using quantile regression on the M-A scatterplots of high-throughput data
PAA (Protein Array Analyzer)
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Multiple comparison test visualization
PANDA Algorithm
Protein annotation data package builder
Presence-Absence Calls from Negative Strand Matching Probesets
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
Generate PanViz visualisations from your pangenome
Predict metabolic pathway activity based on metabolomics data
support for parallelized estimation of GLMs/GEEs
Parametric And Resistant Outlier DYtection
Prediction of pathway-related protein-protein interaction networks
Quantify deregulation of pathways in cancer
An R package for pathway analysis using topological information
PathoStat Statistical Microbiome Analysis Package
Render molecular pathways
Methods to Find Pathways with Significantly Different Variability
a tool set for pathway based data integration and visualization
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Manipulating and exploring protein and proteomics data
Permutation-Based Confidence for Molecular Classification
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
pcaGoPromoter is used to analyze DNA micro array data
A collection of PCA methods
Phenotype Consensus ANalysis (PCAN)
Principal Coordinates and Hotelling's T-Square method
Phenotypes and cellular organizational units
Platform Design Information Package Builder
Classification of Microarray Samples using Penalized Discriminant Methods
Probe-level Expression Change Averaging
Statistical analysis of peptide microarrays
Parsing pepXML files and filter based on peptide FDR.
An package for identification of novel peptides by customized database derived from RNA-Seq
Parametric Gene Set Enrichment Analysis
Analysis of Large-Scale Pharmacogenomic Data
Phenotypic distance measures
Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.
Statistical analysis of phenotypic data
Phylogenetic partitioning based ILR transform for metagenomics data
Handling and analysis of high-throughput microbiome census data
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
Platform for integrative analysis of omics data
Adaptive Gene Picking for Microarray Expression Data Analysis
Probabilistic inference of ChIP-seq
Infers biological signatures from gene expression data
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Pairwise INTegration of functional genomics data
Package Dependency Tools
Statistical tools and data structures for plate-based flow cytometry
R framework for exploration and analysis of respirometry data
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Implements the Affymetrix PLIER algorithm
Local Pooled Error Test for Differential Expression with Paired High-throughput Data
Piecewise Linear Regression Splines (PLRS) for the association between DNA copy number and gene expression
Probe level Locally moderated Weighted t-tests.
Parallel Mixed Model
Position-Dependent Kernel Association Test
Simulate RNA-seq reads
Add-on to DESeq to improve p-values and q-values
Protein-Protein Interaction Statistical Package
Identification of potential quadruplex forming sequences
Data analysis for cell-based functional assays
Probe region expression estimation for RNA-seq data for improved microarray comparability
Position RElated Data Anlysis
Inference for predictive networks designed for (but not limited to) genomic data
A collection of pre-processing functions
Prize: an R package for prioritization estimation based on analytic hierarchy process
Generating SAM file for PSMs in shotgun proteomics data
Ciphergen SELDI-TOF Processing
Prediction of Oligomerization of Coiled Coil Proteins
Protein co-expression network analysis (ProCoNA).
Preprocessing of FIA-HRMS data
Profile score distributions
A unifying bioinformatics framework for spatial proteomics
Interactive visualisation of spatial proteomics data
PRojection Onto the Most Interesting Statistical Evidence
PROspective Power Evaluation for RNAseq
Provides a GUI for DAPAR
Statistical Tools for volume data from 2D Gel Electrophoresis
Protein Profiling
Transform public proteomics data resources into Bioconductor Data Structures
An R package for proteomics data quality control
S4 generic functions for Bioconductor proteomics infrastructure
Population-Specific Expression Analysis.
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Proteomics Standard Initiative Common QUery InterfaCe
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Copy number calling and SNV classification using targeted short read sequencing
PCA-based gene filtering for Affymetrix arrays
Principal Variance Component Analysis (PVCA)
Peptide Annotation and Data Visualization using Gviz
PWM enrichment analysis
Pathway-based data integration of omics data
A Framework for Quality Control
Quantitative DNA sequencing for chromosomal aberrations
Data-driven normalization strategies for high-throughput qPCR data.
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Quick Read Quality Control
IP-seq data analysis and vizualization
Quality Control of Gated Flow Cytometry Experiments
A test for when to use quantile normalization
Quantile smoothing and genomic visualization of array data
Identification of mutational clusters in protein quaternary structures.
Quantify and Annotate Short Reads in R
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
An R package for qualitative biclustering in support of gene co-expression analyses
qusage: Quantitative Set Analysis for Gene Expression
Q-value estimation for false discovery rate control
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
A package for importing and analyzing data from Roche's Genome Sequencer System
An R package for RNA visualization and analysis
Rhythmicity Analysis Incorporating Non-parametric Methods
Robust Analysis of MicroArrays
AmiGO visualize R interface
Randomization routines for Clinical Trials
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Visualization of rare variants in whole genome sequencing data
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Support for Springer monograph on Bioconductor
An interface to the BOOST graph library
RBioinf
Parses BioPax files and represents them in R
RBM: a R package for microarray and RNA-Seq data analysis
R bowtie wrapper
Robust likelihood-based survival modeling with microarray data
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
RNA Centric Annotation System
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
Similarity measures for chemical compounds
Optimyzed Cellular Hierarchies for Flow Cytometry
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Display and manipulate graphs in Cytoscape >= 3.3.0
Display and manipulate graphs in cytoscape.js
Display and manipulate graphs in Cytoscape
An R Package for retrieving data from DAVID into R objects using Web Services API.
R Wrapper for DGIdb
Decomposition of Isotopic Patterns
A package for nonlinear dimension reduction with Isomap and LLE.
Reactome Pathway Analysis
Functionality to Read and Manipulate SomaLogic ADAT files
Read qPCR data
Regional Expression Biases
Explore and download data from the recount project
An R package for the creation of complex genomic profile plots
Interactive visualization and manipulation of nested networks
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
A queryable collection of molecular interactions, from many sources
A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
Association analysis of genomic regions based on permutation tests
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Lasso-Based Methods for Detection of Differential Exon Usage
Epigenomic tools
Tools for making reports in various formats
Recalibrating Quality Of Nucleotides
Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge.
Assign rfPred functional prediction scores to a missense variants list
de novo motif discovery
Make an R function available in the Galaxy web platform
Convert a Graph into a D3js Script
Provides plotting capabilities for R graph objects
Client for GREAT Analysis
Random Gene Set Enrichment Analysis
Gene Set Enrichment / Projection Displays
HDF5 interface to R
HTSlib high-throughput sequencing library as an R package
Hidden Variable Dynamic Modeling
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Analysis of sequencing data from ribosome profiling experiments
RImmPort: Enabling Ready-for-analysis Immunology Research Data
R Investigation of ChIP-chip Oligoarrays
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
Converting experimental metadata from ISA-tab into Bioconductor data structures
A Genotype Calling Algorithm for Affymetrix SNP Arrays
MicroArray Gene-expression-based Program In Error rate estimation
R interface to the MAPPER database of transcription factor binding sites
Workflow to process tandem MS files and build MassBank records
R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
Package to work with miRNAs and miRNA targets with R
Estimate Pairwise Interactions from multidimensional features
Statistical analysis of high-throughput RNAi screens
An R package for analysis of massive parallel sequencing based RNA structure probing data
Benchmarks for RNA-seq Quantification Pipelines
rnaSeq secondary analyses
Sample size for RNAseq studies
RnaSeqSampleSize
RnBeads
R Normalization and Inference of Time Series data
Identify differential APA usage from RNA-seq alignments
utilities for ROC, with uarray focus
Infer miRNA-mRNA interactions using paired expression data from a single sample
Statistical analysis of Solexa sequencing data
An R interface to the Ontology Lookup Service
R Onto-Tools suite
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
Reproducibility-Optimized Test Statistic
RPA: Robust Probabilistic Averaging for probe-level analysis
R interface to PSI-MI 2.5 files
R Interface to the ProteomeXchange Repository
Quality Control Tool for High-Throughput Sequencing Data
Qualitative biclustering algorithm for expression data analysis in R
Interface to the RDP Classifier
Inference on agreement between ordered lists
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
R support for SBML, using libsbml
rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
Subread sequence alignment for R
RSVSim: an R/Bioconductor package for the simulation of structural variations
Interfaces the tandem protein identification algorithm in R
Open-source toolkit to analyse data from xCELLigence System (RTCA)
The Cancer Genome Atlas Data Integration
A new tool for exporting TCGA Firehose data
Reconstruction of transcriptional networks and analysis of master regulators
This package is designed to perform Gene Set Analysis across multiple genomic platforms
R interface to genome browsers and their annotation tracks
Rtreemix: Mutagenetic trees mixture models.
Identification of transcriptional regulatory modules from PPI networks
A shiny user interface for rTRM
Removal of unwanted variation for gene-gene correlations and related analysis
RUV for normalization of expression array data
Remove Unwanted Variation from RNA-Seq Data
Expose R functions as web services through Java/Axis/Apache
S4 implementation of vectors and lists
Significance Analysis of Function and Expression
Collection of functions for reading and comparing SAGE libraries
Statistical Analysis of the GeneChip
Identifies cell population in flow cytometry data.
Tools for Sanger Sequencing Data in R
Spatial Analysis of Network Associations
A package for variant peptides detection and visualization in shotgun proteomics.
Significance Analysis of Prognostic Signatures
Parse and analyze Illumina SAV files
R Client for Seven Bridges Genomics API
SBML-R Interface and Analysis Tools
Single-Cell Consensus Clustering
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Single-cell analysis toolkit for gene expression data in R
Single Cell Differential Expression
In Silico Interactome
Methods for Single-Cell RNA-Seq Data Analysis
SiRNA correction for seed mediated off-target effect
Methods for identifying small RNA loci from high-throughput sequencing data
Functions for analyzing SELEX-seq data
Information Accretion-based Function Predictor Evaluation
SEPA
a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
Big Data Management of Whole-genome Sequence Variant Calls
Estimation of per-position bias in high-throughput sequencing data
Copy number analysis of high-throughput sequencing cancer data
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Sequence logos for DNA sequence alignments
Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
Analysis of nucleotide, sequence and quality content on fastq files.
Tools for variant data
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
Splice event prediction and quantification from RNA-seq data
Interactive visualization for Illumina methylation arrays
Provides a GUI for rTANDEM
FASTQ input and manipulation
Find SNV/Indel differences between two bam files with near relationship
Statistics for Integrative Genomics Analyses in R
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
SigFuge
Multiple testing using SAM and Efron's empirical Bayes approaches
Statistics and dIagnostic Graphs for HTS
Empirical Bayesian approach to mutational signature discovery
Pathway Analysis
Gene signature generation for functionally validated signaling pathways
Integrated Analysis on two human genomic datasets
GC-SIM-MS data processing and alaysis tool
Similar Binding Profiles
Metrics to estimate a level of similarity between two ChIP-Seq profiles
SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
Very simple high level analysis of Affymetrix data
Simulator for Collections of Independent Genomic Data Sets
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
SISPA: Method for Sample Integrated Set Profile Analysis
Sample Size and Power Calculation in Micorarray Studies
The Omegahat interface for R and Java
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
Synthetic Lethal Genetic Interaction
Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
Significance-based Modules Integrating the Transcriptome and Epigenome
Signal-to-Noise applied to Gene Expression Experiments
Segmentation, normalisation and processing of aCGH data.
Supervised Normalization of Microarrays
Visualizations for copy number alterations
Query data from SNPedia
SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
SnpMatrix and XSnpMatrix classes and methods
Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals
SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing
Somatic Signatures
Identification of Mutational Clusters in 3D Protein Space via Simulation.
SPADE -- An analysis and visualization tool for Flow Cytometry
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Condition specific detection from expression data
S-system parameter estimation method
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
Methods for Spike-in Arrays
splicegear
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
A bioconductor package for exploration of alignment gap positions from RNA-seq data
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Splice Interpreter Of Transcripts
Visualization of high-throughput assays in microtitre plate or slide format
Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
Add-on of the SQUAD Software
A compilation of metadata from NCBI SRA and tools
Simplified RNA-Seq Analysis Pipeline
SRGnet An R package for studying synergistic response genes from transcriptomics data
S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
Strength of Selected Codon Usage
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Estimate Microarray Sample Size
General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
A small RNA-seq visualizer and analysis toolkit
The genomic STate ANnotation package
Stability Ranking
StarBioTrek
Simple tiling array analysis of Affymetrix ChIP-chip data
Classes and methods for multi-omics data integration
Statistical Analysis of Metabolite Profile
Stepwise normalization functions for cDNA microarrays
Stepwise Classification of Cancer Samples using High-dimensional Data Sets
Enabling stream processing of large files
STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
Subsampling of high-throughput sequencing count data
SummarizedExperiment container
supraHex: a supra-hexagonal map for analysing tabular omics data
Performance Assessment and Comparison for Survival Analysis
Tools for visualizing genomics data
Surrogate Variable Analysis
SVAPLSseq-An R package to adjust for the hidden factors of variability in differential gene expression studies based on RNAseq data
SVM2CRM: support vector machine for cis-regulatory elements detections
Transform and Filter SWATH Data for Statistical Packages
SWATH extended library generation and satistical data analysis
SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
Switch-like differential expression across single-cell trajectories
Label-free data analysis pipeline for optimal identification and quantitation
Calculate and Visualize Synergy Scores for Drug Combinations
Hits Selection for Synthetic Lethal RNAi Screen Data
systemPipeR: NGS workflow and report generation environment
TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
A package for the analysis of GC-MS metabolite profiling data
TARgeted SEQuencing Experiment Quality Control
TCC: Differential expression analysis for tag count data with robust normalization strategies
TCGAbiolinks: An R/Bioconductor package for integrative analysis with TCGA data
Network reverse engineering from time course data.
Quality control for target capture experiments
Ternary Network Estimation
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Transcription factor Inference through Gaussian process Reconstruction of Expression
Transcript mapping with high-density oligonucleotide tiling arrays
Statistical Analysis for Developmental Microarray Time Course Data
Transcriptome instability analysis
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
R based tk widgets
Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
Package for Topology-based Pathway Analysis of RNASeq data
Enrichment Analysis for Gene Ontology
Analyze thermal proteome profiling (TPP) experiments
Build IGV tracks and HTML reports
A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
Comparison between multiple levels of gene expression
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
GWAS trait-associated SNP enrichment analyses in genomic intervals
Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
Search and visualize intramolecular triplex-forming sequences in DNA
TRONCO, an R package for TRanslational ONCOlogy
TSCAN: Tools for Single-Cell ANalysis
Top Scoring Pairs for Microarray Classification
Transcription Start Site Identification
A fast scatterplot smoother suitable for microarray normalization
TVTB: The VCF Tool Box
RNA-seq data analysis using the Poisson-Tweedie family of distributions
Estimation of local false discovery rate
Import and summarize transcript-level estimates for gene-level analysis
Optional Type Specification Prototype
Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
R Interface to UniProt Web Services
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
uSORT: A self-refining ordering pipeline for gene selection
A Hidden Markov Model for high throughput genotyping arrays
Quantify and interpret divers of variation in multilevel gene expression experiments
Annotation of Genetic Variants
Filtering of coding and non-coding genetic variants
Tools for Working with Genetic Variants
Variational Bayesian Multinomial Probit Regression
An R package for copy number data segmentation
VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
Virtual Inference of Protein-activity by Enriched Regulon analysis
Build virtual array from different microarray platforms
Variance stabilization and calibration for microarray data
variant-transcription factor-phenotype networks
Illumina 450 methylation array normalization and metrics
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
Wavelet-Based Models for Tiling Array Transcriptome Analysis
Tools and extensions for processing Sweave documents
Bioconductor Web Interface
Creates an interactive tcltk widget
Test for differential expression for RNA-seq data
LC/MS and GC/MS Data Analysis
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
Export plotting files to the xmapBridge for visualisation in X:Map
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Representation and manpulation of external sequences
Tools for high-throughput metabolomics
Yet Another Package for Signature Analysis
Affymetrix expression data quality control and reproducibility analysis
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
An R packaged zlib-1.2.5

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