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ABSSeq : ABSSeq: a new RNA-Seq analysis m... (see metadata) ( )

ABarray : Microarray QA and statistical da... (see metadata) ( )

ACME : Algorithms for Calculating Micro... (see metadata) ( )

ADaCGH2 : Analysis of big data from aCGH e... (see metadata) ( )

AGDEX : Agreement of Differential Expression Analysis ( )

AIMS : AIMS : Absolute Assignment of Br... (see metadata) ( )

AMOUNTAIN : Active modules for multilayer we... (see metadata) ( )

ANF : Affinity Network Fusion for Comp... (see metadata) ( )

ASAFE : Ancestry Specific Allele Frequency Estimation ( )

ASEB : Predict Acetylated Lysine Sites ( )

ASGSCA : Association Studies for multiple... (see metadata) ( )

ASSET : An R package for subset-based as... (see metadata) ( )

ASSIGN : Adaptive Signature Selection and... (see metadata) ( )

AffyCompatible : Affymetrix GeneChip software compatibility ( )

AffyExpress : Affymetrix Quality Assessment and Analysis Tool ( )

AffyRNADegradation : Analyze and correct probe positi... (see metadata) ( )

AnalysisPageServer : A framework for sharing interact... (see metadata) ( )

AnnotationDbi : Manipulation of SQLite-based ann... (see metadata) ( )

AnnotationForge : Tools for building SQLite-based ... (see metadata) ( )

AnnotationFuncs : Annotation translation functions ( )

AnnotationHub : Client to access AnnotationHub resources ( )

ArrayExpress : Access the ArrayExpress Microarr... (see metadata) ( )

ArrayTV : Implementation of wave correction for arrays ( )

ArrayTools : geneChip Analysis Package ( )

BAC : Bayesian Analysis of Chip-chip experiment ( )

BADER : Bayesian Analysis of Differentia... (see metadata) ( )

BCRANK : Predicting binding site consensu... (see metadata) ( )

BEclear : Correction of batch effects in D... (see metadata) ( )

BGmix : Bayesian models for differential gene expression ( )

BHC : Bayesian Hierarchical Clustering ( )

BRAIN : Baffling Recursive Algorithm for... (see metadata) ( )

BUS : Gene network reconstruction ( )

BaseSpaceR : R SDK for BaseSpace RESTful API ( )

BayesKnockdown : BayesKnockdown: Posterior Probab... (see metadata) ( )

BayesPeak : Bayesian Analysis of ChIP-seq Data ( )

BeadDataPackR : Compression of Illumina BeadArray data ( )

BiRewire : High-performing routines for the... (see metadata) ( )

BicARE : Biclustering Analysis and Results Exploration ( )

BioCor : Functional similarities ( )

BioMM : BioMM: Biological-informed Multi... (see metadata) ( )

BioMVCClass : Model-View-Controller (MVC) Clas... (see metadata) ( )

BioNet : Routines for the functional anal... (see metadata) ( )

BioQC : Detect tissue heterogeneity in e... (see metadata) ( )

BioSeqClass : Classification for Biological Sequences ( )

Biobase : Biobase: Base functions for Bioconductor ( )

BiocCaseStudies : BiocCaseStudies: Support for the... (see metadata) ( )

BiocCheck : Bioconductor-specific package checks ( )

BiocFileCache : Manage Files Across Sessions ( )

BiocGenerics : S4 generic functions used in Bioconductor ( )

BiocNeighbors : Nearest Neighbor Detection for B... (see metadata) ( )

BiocParallel : Bioconductor facilities for parallel evaluation ( )

BiocPkgTools : Collection of simple tools for l... (see metadata) ( )

BiocSingular : Singular Value Decomposition for... (see metadata) ( )

BiocStyle : Standard styles for vignettes an... (see metadata) ( )

BiocVersion : Set the appropriate version of B... (see metadata) ( )

Biostrings : Efficient manipulation of biological strings ( )

BrainStars : query gene expression data and p... (see metadata) ( )

BridgeDbR : Code for using BridgeDb identifi... (see metadata) ( )

BrowserViz : BrowserViz: interactive R/browse... (see metadata) ( )

BufferedMatrix : A matrix data storage object hel... (see metadata) ( )

BufferedMatrixMethods : Microarray Data related methods ... (see metadata) ( )

CALIB : Calibration model for estimating... (see metadata) ( )

CAnD : Perform Chromosomal Ancestry Dif... (see metadata) ( )

CCPROMISE : PROMISE analysis with Canonical ... (see metadata) ( )

CFAssay : Statistical analysis for the Col... (see metadata) ( )

CGEN : An R package for analysis of cas... (see metadata) ( )

CGHbase : CGHbase: Base functions and clas... (see metadata) ( )

CGHcall : Calling aberrations for array CGH tumor profiles. ( )

CGHnormaliter : Normalization of array CGH data ... (see metadata) ( )

CGHregions : Dimension Reduction for Array CG... (see metadata) ( )

CHRONOS : CHRONOS: A time-varying method f... (see metadata) ( )

CMA : Synthesis of microarray-based classification ( )

CNAnorm : A normalization method for Copy ... (see metadata) ( )

CNORdt : Add-on to CellNOptR: Discretized time treatments ( )

CNORfeeder : Integration of CellNOptR to add missing links ( )

CNORfuzzy : Addon to CellNOptR: Fuzzy Logic ( )

CNORode : ODE add-on to CellNOptR ( )

CNTools : Convert segment data into a regi... (see metadata) ( )

CNVtools : A package to test genetic associ... (see metadata) ( )

COMPASS : Combinatorial Polyfunctionality ... (see metadata) ( )

CONFESS : Cell OrderiNg by FluorEScence Signal ( )

CORREP : Multivariate Correlation Estimat... (see metadata) ( )

COSNet : Cost Sensitive Network for node ... (see metadata) ( )

CRImage : CRImage a package to classify ce... (see metadata) ( )

CSSP : ChIP-Seq Statistical Power ( )

CTDquerier : Package for CTDbase data query, ... (see metadata) ( )

CancerInSilico : An R interface for computational... (see metadata) ( )

CancerMutationAnalysis : Cancer mutation analysis ( )

CancerSubtypes : Cancer subtypes identification, ... (see metadata) ( )

Cardinal : A mass spectrometry imaging tool... (see metadata) ( )

Category : Category Analysis ( )

CausalR : Causal network analysis methods ( )

CellMapper : Predict genes expressed selectiv... (see metadata) ( )

CellNOptR : Training of boolean logic models... (see metadata) ( )

CellScore : Tool for Evaluation of Cell Iden... (see metadata) ( )

ChemmineOB : R interface to a subset of OpenB... (see metadata) ( )

Chicago : CHiCAGO: Capture Hi-C Analysis o... (see metadata) ( )

Clomial : Infers clonal composition of a tumor ( )

Clonality : Clonality testing ( )

ClusterJudge : Judging Quality of Clustering Me... (see metadata) ( )

ClusterSignificance : The ClusterSignificance package ... (see metadata) ( )

CoRegFlux : CoRegFlux ( )

CoRegNet : CoRegNet : reconstruction and in... (see metadata) ( )

CorMut : Detect the correlated mutations ... (see metadata) ( )

Cormotif : Correlation Motif Fit ( )

CountClust : Clustering and Visualizing RNA-S... (see metadata) ( )

CytoDx : Robust prediction of clinical ou... (see metadata) ( )

DART : Denoising Algorithm based on Rel... (see metadata) ( )

DBChIP : Differential Binding of Transcri... (see metadata) ( )

DECIPHER : Tools for curating, analyzing, a... (see metadata) ( )

DEDS : Differential Expression via Dist... (see metadata) ( )

DEGseq : Identify Differentially Expresse... (see metadata) ( )

DESeq : Differential gene expression ana... (see metadata) ( )

DEqMS : a tool to perform statistical an... (see metadata) ( )

DEsingle : DEsingle for detecting three typ... (see metadata) ( )

DFP : Gene Selection ( )

DNABarcodeCompatibility : A Tool for Optimizing Combinatio... (see metadata) ( )

DNABarcodes : A tool for creating and analysin... (see metadata) ( )

DNAcopy : DNA copy number data analysis ( )

DTA : Dynamic Transcriptome Analysis ( )

DeMAND : DeMAND ( )

DelayedArray : A unified framework for working ... (see metadata) ( )

DelayedDataFrame : Delayed operation on DataFrame u... (see metadata) ( )

DelayedMatrixStats : Functions that Apply to Rows and... (see metadata) ( )

DepecheR : Determination of essential pheno... (see metadata) ( )

DiffLogo : DiffLogo: A comparative visualis... (see metadata) ( )

Director : A dynamic visualization tool of multi-level data ( )

DirichletMultinomial : Dirichlet-Multinomial Mixture Mo... (see metadata) ( )

DriverNet : Drivernet: uncovering somatic dr... (see metadata) ( )

DupChecker : a package for checking high-thro... (see metadata) ( )

DynDoc : Dynamic document tools ( )

EBImage : Image processing and analysis toolbox for R ( )

EBSEA : Exon Based Strategy for Expressi... (see metadata) ( )

EBSeq : An R package for gene and isofor... (see metadata) ( )

EBSeqHMM : Bayesian analysis for identifyin... (see metadata) ( )

EBarrays : Unified Approach for Simultaneou... (see metadata) ( )

EBcoexpress : EBcoexpress for Differential Co-... (see metadata) ( )

ELBOW : ELBOW - Evaluating foLd change By the lOgit Way ( )

EMDomics : Earth Movers Distance for Differ... (see metadata) ( )

ENCODExplorer : A compilation of ENCODE metadata ( )

ENVISIONQuery : Retrieval from the ENVISION bioi... (see metadata) ( )

EmpiricalBrownsMethod : Uses Browns method to combine p-... (see metadata) ( )

EnhancedVolcano : Publication-ready volcano plots ... (see metadata) ( )

EpiDISH : Epigenetic Dissection of Intra-S... (see metadata) ( )

ExiMiR : R functions for the normalizatio... (see metadata) ( )

ExperimentHub : Client to access ExperimentHub resources ( )

FELLA : Interpretation and enrichment fo... (see metadata) ( )

FGNet : Functional Gene Networks derived... (see metadata) ( )

FISHalyseR : FISHalyseR a package for automat... (see metadata) ( )

FRGEpistasis : Epistasis Analysis for Quantitat... (see metadata) ( )

FamAgg : Pedigree Analysis and Familial Aggregation ( )

FindMyFriends : Microbial Comparative Genomics in R ( )

FitHiC : Confidence estimation for intra-... (see metadata) ( )

FlowRepositoryR : FlowRepository R Interface ( )

FlowSOM : Using self-organizing maps for v... (see metadata) ( )

GAprediction : Prediction of gestational age wi... (see metadata) ( )

GEM : GEM: fast association study for ... (see metadata) ( )

GENIE3 : GEne Network Inference with Ensemble of trees ( )

GEOmetadb : A compilation of metadata from NCBI GEO ( )

GEOquery : Get data from NCBI Gene Expression Omnibus (GEO) ( )

GEOsubmission : Prepares microarray data for submission to GEO ( )

GEWIST : Gene Environment Wide Interaction Search Threshold ( )

GIGSEA : Genotype Imputed Gene Set Enrichment Analysis ( )

GISPA : GISPA: Method for Gene Integrate... (see metadata) ( )

GLAD : Gain and Loss Analysis of DNA ( )

GOexpress : Visualise microarray and RNAseq ... (see metadata) ( )

GOsummaries : Word cloud summaries of GO enrichment analysis ( )

GRENITS : Gene Regulatory Network Inferenc... (see metadata) ( )

GRridge : Better prediction by use of co-d... (see metadata) ( )

GSALightning : Fast Permutation-based Gene Set Analysis ( )

GSAR : Gene Set Analysis in R ( )

GSCA : GSCA: Gene Set Context Analysis ( )

GSEABase : Gene set enrichment data structures and methods ( )

GSEAlm : Linear Model Toolset for Gene Se... (see metadata) ( )

GSRI : Gene Set Regulation Index ( )

GSVA : Gene Set Variation Analysis for ... (see metadata) ( )

GWASTools : Tools for Genome Wide Association Studies ( )

GateFinder : Projection-based Gating Strategy... (see metadata) ( )

GenRank : Candidate gene prioritization ba... (see metadata) ( )

GeneAccord : Detection of clonally exclusive ... (see metadata) ( )

GeneAnswers : Integrated Interpretation of Genes ( )

GeneGA : Design gene based on both mRNA s... (see metadata) ( )

GeneMeta : MetaAnalysis for High Throughput Experiments ( )

GeneNetworkBuilder : GeneNetworkBuilder: a bioconduct... (see metadata) ( )

GeneOverlap : Test and visualize gene overlaps ( )

GeneRegionScan : GeneRegionScan ( )

GeneSelectMMD : Gene selection based on the marg... (see metadata) ( )

GeneticsDesign : Functions for designing genetics studies ( )

GeneticsPed : Pedigree and genetic relationship functions ( )

GenomeGraphs : Plotting genomic information from Ensembl ( )

Genominator : Analyze, manage and store genomic data ( )

GladiaTOX : R Package for Processing High Co... (see metadata) ( )

Glimma : Interactive HTML graphics ( )

GlobalAncova : Global test for groups of variab... (see metadata) ( )

GraphAT : Graph Theoretic Association Tests ( )

GraphAlignment : GraphAlignment ( )

GraphPAC : Identification of Mutational Clu... (see metadata) ( )

HCABrowser : Browse the Human Cell Atlas data portal ( )

HDF5Array : HDF5 backend for DelayedArray objects ( )

HDTD : Statistical Inference about the ... (see metadata) ( )

HELP : Tools for HELP data analysis ( )

HEM : Heterogeneous error model for id... (see metadata) ( )

HIBAG : HLA Genotype Imputation with Attribute Bagging ( )

HIREewas : Detection of cell-type-specific ... (see metadata) ( )

HMMcopy : Copy number prediction with corr... (see metadata) ( )

HPAanalyze : Retrieve and analyze data from t... (see metadata) ( )

HTSanalyzeR : Gene set over-representation, en... (see metadata) ( )

HTqPCR : Automated analysis of high-throughput qPCR data ( )

Harman : The removal of batch effects fro... (see metadata) ( )

Harshlight : A corrective make-up program for microarray chips ( )

Heatplus : Heatmaps with row and/or column ... (see metadata) ( )

HilbertVis : Hilbert curve visualization ( )

HilbertVisGUI : HilbertVisGUI ( )

HybridMTest : Hybrid Multiple Testing ( )

IHW : Independent Hypothesis Weighting ( )

IMMAN : Interlog protein network reconst... (see metadata) ( )

IMPCdata : Retrieves data from IMPC database ( )

INDEED : An Implementation of Integrated ... (see metadata) ( )

INPower : An R package for computing the n... (see metadata) ( )

IPPD : Isotopic peak pattern deconvolut... (see metadata) ( )

IRanges : Foundation of integer range mani... (see metadata) ( )

ISoLDE : Integrative Statistics of alleLe... (see metadata) ( )

Icens : NPMLE for Censored and Truncated Data ( )

IdMappingAnalysis : ID Mapping Analysis ( )

IdMappingRetrieval : ID Mapping Data Retrieval ( )

ImpulseDE : Detection of DE genes in time se... (see metadata) ( )

IntramiRExploreR : Predicting Targets for Drosophil... (see metadata) ( )

IsoCorrectoR : Correction for natural isotope a... (see metadata) ( )

IsoCorrectoRGUI : Graphical User Interface for IsoCorrectoR ( )

IsoGeneGUI : A graphical user interface to co... (see metadata) ( )

KCsmart : Multi sample aCGH analysis packa... (see metadata) ( )

KEGGREST : Client-side REST access to KEGG ( )

KEGGgraph : KEGGgraph: A graph approach to K... (see metadata) ( )

KinSwingR : KinSwingR: network-based kinase ... (see metadata) ( )

LBE : Estimation of the false discovery rate. ( )

LEA : LEA: an R package for Landscape ... (see metadata) ( )

LMGene : LMGene Software for Data Transfo... (see metadata) ( )

LPE : Methods for analyzing microarray... (see metadata) ( )

LPEadj : A correction of the local pooled... (see metadata) ( )

LRBaseDbi : DBI to construct LRBase-related package ( )

LVSmiRNA : LVS normalization for Agilent miRNA data ( )

LedPred : Learning from DNA to Predict Enhancers ( )

Linnorm : Linear model and normality based... (see metadata) ( )

Logolas : EDLogo Plots Featuring String Lo... (see metadata) ( )

M3C : Monte Carlo Reference-based Consensus Clustering ( )

M3Drop : Michaelis-Menten Modelling of Dr... (see metadata) ( )

MANOR : CGH Micro-Array NORmalization ( )

MBAmethyl : Model-based analysis of DNA methylation data ( )

MBCB : MBCB (Model-based Background Cor... (see metadata) ( )

MBttest : Multiple Beta t-Tests ( )

MEDME : Modelling Experimental Data from MeDIP Enrichment ( )

MEIGOR : MEIGO - MEtaheuristics for bIoin... (see metadata) ( )

MGFM : Marker Gene Finder in Microarray... (see metadata) ( )

MGFR : Marker Gene Finder in RNA-seq data ( )

MIMOSA : Mixture Models for Single-Cell Assays ( )

MLP : MLP ( )

MPFE : Estimation of the amplicon methy... (see metadata) ( )

MSGFgui : A shiny GUI for MSGFplus ( )

MSGFplus : An interface between R and MS-GF+ ( )

MSstats : Protein Significance Analysis in... (see metadata) ( )

MSstatsTMT : Protein Significance Analysis in... (see metadata) ( )

MVCClass : Model-View-Controller (MVC) Classes ( )

MantelCorr : Compute Mantel Cluster Correlations ( )

MassArray : Analytical Tools for MassArray Data ( )

MassSpecWavelet : Mass spectrum processing by wave... (see metadata) ( )

MaxContrastProjection : Perform a maximum contrast proje... (see metadata) ( )

MeSHDbi : DBI to construct MeSH-related pa... (see metadata) ( )

MeasurementError_cor : Measurement Error model estimate... (see metadata) ( )

MergeMaid : Merge Maid ( )

Mergeomics : Integrative network analysis of omics data ( )

MetCirc : Navigating mass spectral similar... (see metadata) ( )

MetaCyto : MetaCyto: A package for meta-ana... (see metadata) ( )

MethPed : A DNA methylation classifier too... (see metadata) ( )

MethylMix : MethylMix: Identifying methylati... (see metadata) ( )

Mfuzz : Soft clustering of time series g... (see metadata) ( )

MiChip : MiChip Parsing and Summarizing Functions ( )

MiPP : Misclassification Penalized Post... (see metadata) ( )

MiRaGE : MiRNA Ranking by Gene Expression ( )

Mirsynergy : Mirsynergy ( )

MmPalateMiRNA : Murine Palate miRNA Expression Analysis ( )

MoPS : MoPS - Model-based Periodicity Screening ( )

Mulcom : Calculates Mulcom test ( )

MultiMed : Testing multiple biological medi... (see metadata) ( )

NBSplice : Negative Binomial Models to dete... (see metadata) ( )

NOISeq : Exploratory analysis and differe... (see metadata) ( )

NTW : Predict gene network using an Or... (see metadata) ( )

NanoStringDiff : Differential Expression Analysis... (see metadata) ( )

NeighborNet : Neighbor_net analysis ( )

NetSAM : Network Seriation And Modularization ( )

NormqPCR : Functions for normalisation of RT-qPCR data ( )

NuPoP : An R package for nucleosome positioning prediction ( )

OCplus : Operating characteristics plus s... (see metadata) ( )

OGSA : Outlier Gene Set Analysis ( )

OLIN : Optimized local intensity-depend... (see metadata) ( )

OLINgui : Graphical user interface for OLIN ( )

OPWeight : Optimal p-value weighting with i... (see metadata) ( )

OSAT : OSAT: Optimal Sample Assignment Tool ( )

OmicsMarkeR : Classification and Feature Selec... (see metadata) ( )

Onassis : OnASSIs Ontology Annotation and ... (see metadata) ( )

OncoScore : A tool to identify potentially oncogenic genes ( )

OncoSimulR : Forward Genetic Simulation of Ca... (see metadata) ( )

OrderedList : Similarities of Ordered Gene Lists ( )

Oscope : Oscope - A statistical pipeline ... (see metadata) ( )

OutlierD : Outlier detection using quantile... (see metadata) ( )

PANR : Posterior association networks a... (see metadata) ( )

PCAN : Phenotype Consensus ANalysis (PCAN) ( )

PCAtools : PCAtools: everything Principal Components Analysis ( )

PECA : Probe-level Expression Change Averaging ( )

PLPE : Local Pooled Error Test for Diff... (see metadata) ( )

POST : Projection onto Orthogonal Space... (see metadata) ( )

PREDA : Position Related Data Analysis ( )

PROMISE : PRojection Onto the Most Interes... (see metadata) ( )

PROPER : PROspective Power Evaluation for RNAseq ( )

PROPS : PRObabilistic Pathway Score (PROPS) ( )

PROcess : Ciphergen SELDI-TOF Processing ( )

PSEA : Population-Specific Expression Analysis. ( )

PSICQUIC : Proteomics Standard Initiative C... (see metadata) ( )

PWMEnrich : PWM enrichment analysis ( )

Path2PPI : Prediction of pathway-related pr... (see metadata) ( )

PathNet : An R package for pathway analysi... (see metadata) ( )

PepsNMR : Pre-process 1H-NMR FID signals ( )

PharmacoGx : Analysis of Large-Scale Pharmacogenomic Data ( )

PhenStat : Statistical analysis of phenotypic data ( )

Polyfit : Add-on to DESeq to improve p-values and q-values ( )

Prize : Prize: an R package for prioriti... (see metadata) ( )

ProtGenerics : S4 generic functions for Biocond... (see metadata) ( )

ProteoMM : Multi-Dataset Model-based Differ... (see metadata) ( )

QSutils : Quasispecies Diversity ( )

QuartPAC : Identification of mutational clu... (see metadata) ( )

QuaternaryProd : Computes the Quaternary Dot Prod... (see metadata) ( )

R4RNA : An R package for RNA visualization and analysis ( )

RBGL : An interface to the BOOST graph library ( )

RBM : RBM: a R package for microarray ... (see metadata) ( )

RBioinf : RBioinf ( )

RCASPAR : A package for survival time pred... (see metadata) ( )

RCM : Fit row-column association model... (see metadata) ( )

RCyjs : Display and manipulate graphs in cytoscape.js ( )

RDRToolbox : A package for nonlinear dimensio... (see metadata) ( )

REBET : The subREgion-based BurdEn Test (REBET) ( )

RGSEA : Random Gene Set Enrichment Analysis ( )

RGalaxy : Make an R function available in ... (see metadata) ( )

RIVER : R package for RIVER (RNA-Informe... (see metadata) ( )

RImmPort : RImmPort: Enabling Ready-for-ana... (see metadata) ( )

RNASeqPower : Sample size for RNAseq studies ( )

RNAdecay : Maximum Likelihood Decay Modelin... (see metadata) ( )

RNAinteract : Estimate Pairwise Interactions f... (see metadata) ( )

ROC : utilities for ROC, with uarray focus ( )

ROTS : Reproducibility-Optimized Test Statistic ( )

ROntoTools : R Onto-Tools suite ( )

RPA : RPA: Robust Probabilistic Averag... (see metadata) ( )

RProtoBufLib : C++ headers and static libraries... (see metadata) ( )

RRHO : Inference on agreement between ordered lists ( )

RSeqAn : R SeqAn ( )

RTCA : Open-source toolkit to analyse d... (see metadata) ( )

RTCGA : The Cancer Genome Atlas Data Integration ( )

RTopper : This package is designed to perf... (see metadata) ( )

RVS : Computes estimates of the probab... (see metadata) ( )

RandomWalkRestartMH : Random walk with restart on mult... (see metadata) ( )

RankProd : Rank Product method for identify... (see metadata) ( )

RbcBook1 : Support for Springer monograph on Bioconductor ( )

Rbowtie : R bowtie wrapper ( )

Rbowtie2 : An R Wrapper for Bowtie2 and AdapterRemoval ( )

RchyOptimyx : Optimyzed Cellular Hierarchies for Flow Cytometry ( )

Rdisop : Decomposition of Isotopic Patterns ( )

ReadqPCR : Read qPCR data ( )

RedeR : Interactive visualization and ma... (see metadata) ( )

RefNet : A queryable collection of molecu... (see metadata) ( )

RefPlus : A function set for the Extrapola... (see metadata) ( )

Rgin : gin in R ( )

Rgraphviz : Provides plotting capabilities for R graph objects ( )

Rhdf5lib : hdf5 library as an R package ( )

Ringo : R Investigation of ChIP-chip Oligoarrays ( )

Rmagpie : MicroArray Gene-expression-based... (see metadata) ( )

Rnits : R Normalization and Inference of Time Series data ( )

Roleswitch : Infer miRNA-mRNA interactions us... (see metadata) ( )

RpsiXML : R interface to PSI-MI 2.5 files ( )

Rsubread : Subread Sequence Alignment and Counting for R ( )

Rtreemix : Rtreemix: Mutagenetic trees mixture models. ( )

S4Vectors : Foundation of vector-like and li... (see metadata) ( )

SAGx : Statistical Analysis of the GeneChip ( )

SANTA : Spatial Analysis of Network Associations ( )

SBMLR : SBML-R Interface and Analysis Tools ( )

SCAN_UPC : Single-channel array normalizati... (see metadata) ( )

SCBN : A statistical normalization meth... (see metadata) ( )

SELEX : Functions for analyzing SELEX-seq data ( )

SEPIRA : Systems EPigenomics Inference of... (see metadata) ( )

SIAMCAT : Statistical Inference of Associa... (see metadata) ( )

SIM : Integrated Analysis on two human genomic datasets ( )

SIMAT : GC-SIM-MS data processing and alaysis tool ( )

SIMD : Statistical Inferences with MeDI... (see metadata) ( )

SIMLR : Single-cell Interpretation via M... (see metadata) ( )

SISPA : SISPA: Method for Sample Integra... (see metadata) ( )

SLqPCR : Functions for analysis of real-t... (see metadata) ( )

SMAD : Statistical Modelling of AP-MS Data (SMAD) ( )

SMAP : A Segmental Maximum A Posteriori... (see metadata) ( )

SNPRelate : Parallel Computing Toolset for R... (see metadata) ( )

SNPediaR : Query data from SNPedia ( )

SPEM : S-system parameter estimation method ( )

SPIA : Signaling Pathway Impact Analysi... (see metadata) ( )

SPONGE : Sparse Partial Correlations On Gene Expression ( )

SQUADD : Add-on of the SQUAD Software ( )

SRAdb : A compilation of metadata from NCBI SRA and tools ( )

SRGnet : SRGnet: An R package for studyin... (see metadata) ( )

SSPA : General Sample Size and Power An... (see metadata) ( )

STATegRa : Classes and methods for multi-om... (see metadata) ( )

STRINGdb : STRINGdb (Search Tool for the Re... (see metadata) ( )

STROMA4 : Assign Properties to TNBC Patients ( )

SWATH2stats : Transform and Filter SWATH Data ... (see metadata) ( )

SamSPECTRAL : Identifies cell population in flow cytometry data. ( )

Sconify : A toolkit for performing KNN-bas... (see metadata) ( )

SeqGSEA : Gene Set Enrichment Analysis (GS... (see metadata) ( )

SimBindProfiles : Similar Binding Profiles ( )

SpacePAC : Identification of Mutational Clu... (see metadata) ( )

SpeCond : Condition specific detection from expression data ( )

Starr : Simple tiling array analysis of ... (see metadata) ( )

Streamer : Enabling stream processing of large files ( )

Structstrings : Implementation of the dot bracke... (see metadata) ( )

SubCellBarCode : SubCellBarCode: Integrated workf... (see metadata) ( )

Sushi : Tools for visualizing genomics data ( )

SwathXtend : SWATH extended library generatio... (see metadata) ( )

SwimR : SwimR: A Suite of Analytical Too... (see metadata) ( )

SynMut : SynMut: Designing Synonymously M... (see metadata) ( )

TDARACNE : Network reverse engineering from time course data. ( )

TFutils : TFutils ( )

TMixClust : Time Series Clustering of Gene E... (see metadata) ( )

TPP2D : FDR-controlled analysis of 2D-TPP experiments ( )

TRONCO : TRONCO, an R package for TRanslational ONCOlogy ( )

TSCAN : TSCAN: Tools for Single-Cell ANalysis ( )

TSSi : Transcription Start Site Identification ( )

TargetScore : TargetScore: Infer microRNA targ... (see metadata) ( )

TargetSearch : A package for the analysis of GC... (see metadata) ( )

TurboNorm : A fast scatterplot smoother suit... (see metadata) ( )

TypeInfo : Optional Type Specification Prototype ( )

UNDO : Unsupervised Deconvolution of Tu... (see metadata) ( )

UniProt_ws : R Interface to UniProt Web Services ( )

Vega : An R package for copy number data segmentation ( )

VennDetail : A package for visualization and extract details ( )

Wrench : Wrench normalization for sparse count data ( )

XDE : XDE: a Bayesian hierarchical mod... (see metadata) ( )

XINA : Multiplexes isobaric mass tagged... (see metadata) ( )

XVector : Foundation of external vector re... (see metadata) ( )

a4Core : Automated Affymetrix Array Analysis Core Package ( )

a4Preproc : Automated Affymetrix Array Analy... (see metadata) ( )

aCGH : Classes and functions for Array ... (see metadata) ( )

abseqR : Reporting and data analysis func... (see metadata) ( )

acde : Artificial Components Detection ... (see metadata) ( )

affxparser : Affymetrix File Parsing SDK ( )

affy : Methods for Affymetrix Oligonucleotide Arrays ( )

affyILM : Linear Model of background subtr... (see metadata) ( )

affyPLM : Methods for fitting probe-level models ( )

affyPara : Parallelized preprocessing metho... (see metadata) ( )

affyQCReport : QC Report Generation for affyBatch objects ( )

affycomp : Graphics Toolbox for Assessment ... (see metadata) ( )

affyio : Tools for parsing Affymetrix data files ( )

affylmGUI : GUI for limma Package with Affymetrix Microarrays ( )

affypdnn : Probe Dependent Nearest Neighbou... (see metadata) ( )

agilp : Agilent expression array processing package ( )

alevinQC : Generate QC Reports For Alevin Output ( )

alsace : ALS for the Automatic Chemical E... (see metadata) ( )

altcdfenvs : alternative CDF environments (ak... (see metadata) ( )

annotate : Annotation for microarrays ( )

annotationTools : Annotate microarrays and perform... (see metadata) ( )

anota : ANalysis Of Translational Activity (ANOTA). ( )

antiProfiles : Implementation of gene expression anti-profiles ( )

aroma_light : Light-Weight Methods for Normali... (see metadata) ( )

arrayQuality : Assessing array quality on spotted arrays ( )

bacon : Controlling bias and inflation i... (see metadata) ( )

bcSeq : Fast Sequence Mapping in High-Th... (see metadata) ( )

beachmat : Compiling Bioconductor to Handle Each Matrix Type ( )

beadarraySNP : Normalization and reporting of I... (see metadata) ( )

bgafun : BGAfun A method to identify spec... (see metadata) ( )

bgx : Bayesian Gene eXpression ( )

bigPint : Big multivariate data plotted interactively ( )

bigmemoryExtras : An extension of the bigmemory pa... (see metadata) ( )

bioDist : Different distance measures ( )

biobroom : Turn Bioconductor objects into tidy data frames ( )

biocGraph : Graph examples and use cases in Bioinformatics ( )

biocViews : Categorized views of R package repositories ( )

biomaRt : Interface to BioMart databases (i.e. Ensembl) ( )

biomformat : An interface package for the BIOM file format ( )

biosigner : Signature discovery from omics data ( )

biosvd : Package for high-throughput data... (see metadata) ( )

birta : Bayesian Inference of Regulation... (see metadata) ( )

brainImageR : A Framework for visualizing gene... (see metadata) ( )

bridge : Bayesian Robust Inference for Di... (see metadata) ( )

cTRAP : Identification of candidate caus... (see metadata) ( )

caOmicsV : Visualization of multi-dimention... (see metadata) ( )

cancerclass : Development and validation of di... (see metadata) ( )

cbaf : Automated functions for comparin... (see metadata) ( )

ccrepe : ccrepe_and_nc.score ( )

cellGrowth : Fitting cell population growth models ( )

cellHTS2 : Analysis of cell-based screens -... (see metadata) ( )

cellscape : Explores single cell copy number... (see metadata) ( )

cghMCR : Find chromosome regions showing ... (see metadata) ( )

chopsticks : The snp.matrix and X.snp.matrix Classes ( )

cisPath : Visualization and management of ... (see metadata) ( )

cleaver : Cleavage of Polypeptide Sequences ( )

clippda : A package for the clinical prote... (see metadata) ( )

clonotypeR : High throughput analysis of T ce... (see metadata) ( )

clst : Classification by local similarity threshold ( )

clstutils : Tools for performing taxonomic assignment. ( )

clustComp : Clustering Comparison Package ( )

clusterStab : Compute cluster stability scores... (see metadata) ( )

cn_farms : cn.FARMS - factor analysis for c... (see metadata) ( )

coGPS : cancer outlier Gene Profile Sets ( )

coRdon : Codon Usage Analysis and Predict... (see metadata) ( )

codelink : Manipulation of Codelink microarray data ( )

cogena : co-expressed gene-set enrichment analysis ( )

compcodeR : RNAseq data simulation, differen... (see metadata) ( )

condcomp : Condition Comparison in scRNA-seq Data ( )

consensus : Cross-platform consensus analysi... (see metadata) ( )

consensusOV : Gene expression-based subtype cl... (see metadata) ( )

convert : Convert Microarray Data Objects ( )

copa : Functions to perform cancer outl... (see metadata) ( )

covEB : Empirical Bayes estimate of bloc... (see metadata) ( )

covRNA : Multivariate Analysis of Transcriptomic Data ( )

cqn : Conditional quantile normalization ( )

ctc : Cluster and Tree Conversion. ( )

ctsGE : Clustering of Time Series Gene Expression data ( )

cycle : Significance of periodic express... (see metadata) ( )

cytofast : cytofast - A quick visualization... (see metadata) ( )

cytolib : C++ infrastructure for represent... (see metadata) ( )

daMA : Efficient design and analysis of... (see metadata) ( )

dcGSA : Distance-correlation based Gene ... (see metadata) ( )

dcanr : Differential co-expression/assoc... (see metadata) ( )

ddCt : The ddCt Algorithm for the Analy... (see metadata) ( )

decontam : Identify Contaminants in Marker-... (see metadata) ( )

deltaGseg : deltaGseg ( )

derfinderHelper : derfinder helper package ( )

dexus : DEXUS - Identifying Differential... (see metadata) ( )

diffGeneAnalysis : Performs differential gene expression Analysis ( )

diggit : Inference of Genetic Variants Dr... (see metadata) ( )

discordant : The Discordant Method: A Novel A... (see metadata) ( )

dks : The double Kolmogorov-Smirnov pa... (see metadata) ( )

drawProteins : Package to Draw Protein Schemati... (see metadata) ( )

dualKS : Dual KS Discriminant Analysis and Classification ( )

dupRadar : Assessment of duplication rates ... (see metadata) ( )

dyebias : The GASSCO method for correcting... (see metadata) ( )

ecolitk : Meta-data and tools for E. coli ( )

edge : Extraction of Differential Gene Expression ( )

edgeR : Empirical Analysis of Digital Ge... (see metadata) ( )

eisa : Expression data analysis via the... (see metadata) ( )

epiNEM : epiNEM ( )

epivizrServer : WebSocket server infrastructure ... (see metadata) ( )

erccdashboard : Assess Differential Gene Express... (see metadata) ( )

esetVis : Visualizations of expressionSet ... (see metadata) ( )

explorase : GUI for exploratory data analysi... (see metadata) ( )

fCI : f-divergence Cutoff Index for Di... (see metadata) ( )

fabia : FABIA: Factor Analysis for Bicluster Acquisition ( )

factDesign : Factorial designed microarray experiment analysis ( )

farms : FARMS - Factor Analysis for Robu... (see metadata) ( )

fdrame : FDR adjustments of Microarray Ex... (see metadata) ( )

fgsea : Fast Gene Set Enrichment Analysis ( )

flowAI : Automatic and interactive qualit... (see metadata) ( )

flowBeads : flowBeads: Analysis of flow bead data ( )

flowBin : Combining multitube flow cytometry data by binning ( )

flowCHIC : Analyze flow cytometric data usi... (see metadata) ( )

flowCL : Semantic labelling of flow cytom... (see metadata) ( )

flowClean : flowClean ( )

flowClust : Clustering for Flow Cytometry ( )

flowCore : flowCore: Basic structures for flow cytometry data ( )

flowCyBar : Analyze flow cytometric data usi... (see metadata) ( )

flowFP : Fingerprinting for Flow Cytometry ( )

flowFit : Estimate proliferation in cell-t... (see metadata) ( )

flowMap : Mapping cell populations in flow... (see metadata) ( )

flowMatch : Matching and meta-clustering in flow cytometry ( )

flowMeans : Non-parametric Flow Cytometry Data Gating ( )

flowMerge : Cluster Merging for Flow Cytometry Data ( )

flowPeaks : An R package for flow data clustering ( )

flowPloidy : Analyze flow cytometer data to d... (see metadata) ( )

flowPlots : flowPlots: analysis plots and da... (see metadata) ( )

flowQB : Automated Quadratic Characteriza... (see metadata) ( )

flowTime : Annotation and analysis of biolo... (see metadata) ( )

flowTrans : Parameter Optimization for Flow ... (see metadata) ( )

flowType : Phenotyping Flow Cytometry Assays ( )

flowUtils : Utilities for flow cytometry ( )

flowViz : Visualization for flow cytometry ( )

flowcatchR : Tools to analyze in vivo microsc... (see metadata) ( )

focalCall : Detection of focal aberrations i... (see metadata) ( )

frma : Frozen RMA and Barcode ( )

frmaTools : Frozen RMA Tools ( )

gCMAP : Tools for Connectivity Map-like analyses ( )

gCMAPWeb : A web interface for gene-set enrichment analyses ( )

gaga : GaGa hierarchical model for high... (see metadata) ( )

gage : Generally Applicable Gene-set En... (see metadata) ( )

gaggle : Broadcast data between R and Gaggle ( )

gaia : GAIA: An R package for genomic a... (see metadata) ( )

garfield : GWAS Analysis of Regulatory or F... (see metadata) ( )

gcatest : Genotype Conditional Association TEST ( )

gcrma : Background Adjustment Using Sequence Information ( )

gdsfmt : R Interface to CoreArray Genomic... (see metadata) ( )

geNetClassifier : Classify diseases and build asso... (see metadata) ( )

genArise : Microarray Analysis tool ( )

geneClassifiers : Application of gene classifiers ( )

geneRecommender : A gene recommender algorithm to ... (see metadata) ( )

genefilter : genefilter: methods for filterin... (see metadata) ( )

genefu : Computation of Gene Expression-B... (see metadata) ( )

geneplast : Evolutionary and plasticity anal... (see metadata) ( )

geneplotter : Graphics related functions for Bioconductor ( )

genoCN : genotyping and copy number study tools ( )

genomes : Genome sequencing project metadata ( )

gep2pep : Creation and Analysis of Pathway... (see metadata) ( )

gespeR : Gene-Specific Phenotype EstimatoR ( )

ggtree : an R package for visualization a... (see metadata) ( )

globalSeq : Global Test for Counts ( )

globaltest : Testing Groups of Covariates/Fea... (see metadata) ( )

gpls : Classification using generalized... (see metadata) ( )

gprege : Gaussian Process Ranking and Est... (see metadata) ( )

graper : Adaptive penalization in high-di... (see metadata) ( )

graph : graph: A package to handle graph data structures ( )

graphite : GRAPH Interaction from pathway T... (see metadata) ( )

hapFabia : hapFabia: Identification of very... (see metadata) ( )

hicrep : Measuring the reproducibility of Hi-C data ( )

hierGWAS : Asessing statistical significanc... (see metadata) ( )

hierinf : Hierarchical Inference ( )

hmdbQuery : utilities for exploration of hum... (see metadata) ( )

hopach : Hierarchical Ordered Partitionin... (see metadata) ( )

hpar : Human Protein Atlas in R ( )

hypeR : Hyper Enrichment ( )

hyperdraw : Visualizing Hypergaphs ( )

hypergraph : A package providing hypergraph data structures ( )

iASeq : iASeq: integrating multiple sequ... (see metadata) ( )

iBBiG : Iterative Binary Biclustering of Genesets ( )

iCARE : A Tool for Individualized Cohere... (see metadata) ( )

iCOBRA : Comparison and Visualization of ... (see metadata) ( )

iChip : Bayesian Modeling of ChIP-chip D... (see metadata) ( )

iClusterPlus : Integrative clustering of multi-type genomic data ( )

iGC : An integrated analysis package o... (see metadata) ( )

iPAC : Identification of Protein Amino acid Clustering ( )

iSeq : Bayesian Hierarchical Modeling o... (see metadata) ( )

idiogram : idiogram ( )

illuminaio : Parsing Illumina Microarray Output Files ( )

imageHTS : Analysis of high-throughput micr... (see metadata) ( )

immunoClust : immunoClust - Automated Pipeline... (see metadata) ( )

impute : impute: Imputation for microarray data ( )

interactiveDisplay : Package for enabling powerful sh... (see metadata) ( )

interactiveDisplayBase : Base package for enabling powerf... (see metadata) ( )

inveRsion : Inversions in genotype data ( )

isobar : Analysis and quantitation of iso... (see metadata) ( )

iterClust : Iterative Clustering ( )

iterativeBMA : The Iterative Bayesian Model Ave... (see metadata) ( )

iterativeBMAsurv : The Iterative Bayesian Model Ave... (see metadata) ( )

joda : JODA algorithm for quantifying g... (see metadata) ( )

kebabs : Kernel-Based Analysis Of Biological Sequences ( )

kimod : A k-tables approach to integrate... (see metadata) ( )

lapmix : Laplace Mixture Model in Microarray Experiments ( )

les : Identifying Differential Effects... (see metadata) ( )

levi : Landscape Expression Visualization Interface ( )

lfa : Logistic Factor Analysis for Categorical Data ( )

limma : Linear Models for Microarray Data ( )

limmaGUI : GUI for limma Package With Two Color Microarrays ( )

logicFS : Identification of SNP Interactions ( )

logitT : logit-t Package ( )

lol : Lots Of Lasso ( )

lpNet : Linear Programming Model for Network Inference ( )

lpsymphony : Symphony integer linear programming solver in R ( )

maCorrPlot : Visualize artificial correlation... (see metadata) ( )

maSigPro : Significant Gene Expression Prof... (see metadata) ( )

maanova : Tools for analyzing Micro Array experiments ( )

macat : MicroArray Chromosome Analysis Tool ( )

made4 : Multivariate analysis of microar... (see metadata) ( )

maftools : Summarize, Analyze and Visualize MAF Files ( )

maigesPack : Functions to handle cDNA microar... (see metadata) ( )

makecdfenv : CDF Environment Maker ( )

manta : Microbial Assemblage Normalized ... (see metadata) ( )

mapscape : mapscape ( )

marray : Exploratory analysis for two-col... (see metadata) ( )

martini : GWAS Incorporating Networks ( )

maskBAD : Masking probes with binding affinity differences ( )

massiR : massiR: MicroArray Sample Sex Identifier ( )

matchBox : Utilities to compute, compare, a... (see metadata) ( )

matter : A framework for rapid prototypin... (see metadata) ( )

mdp : Molecular Degree of Perturbation... (see metadata) ( )

mdqc : Mahalanobis Distance Quality Con... (see metadata) ( )

messina : Single-gene classifiers and outl... (see metadata) ( )

metaArray : Integration of Microarray Data for Meta-analysis ( )

metaCCA : Summary Statistics-Based Multiva... (see metadata) ( )

metaSeq : Meta-analysis of RNA-Seq count d... (see metadata) ( )

metabomxtr : A package to run mixture models ... (see metadata) ( )

metagenomeFeatures : Exploration of marker-gene seque... (see metadata) ( )

metagenomeSeq : Statistical analysis for sparse ... (see metadata) ( )

metahdep : Hierarchical Dependence in Meta-Analysis ( )

methVisual : Methods for visualization and st... (see metadata) ( )

methylMnM : detect different methylation level (DMR) ( )

mfa : Bayesian hierarchical mixture of... (see metadata) ( )

mgsa : Model-based gene set analysis ( )

miRBaseConverter : A comprehensive and high-efficie... (see metadata) ( )

miRNApath : miRNApath: Pathway Enrichment fo... (see metadata) ( )

miRNAtap : miRNAtap: microRNA Targets - Agg... (see metadata) ( )

microRNA : Data and functions for dealing with microRNAs ( )

microbiome : Microbiome Analytics ( )

mimager : mimager: The Microarray Imager ( )

minet : Mutual Information NETworks ( )

mixOmics : Omics Data Integration Project ( )

mnem : Mixture Nested Effects Models ( )

mogsa : Multiple omics data integrative ... (see metadata) ( )

motifcounter : R package for analysing TFBSs in DNA sequences ( )

msPurity : Automated Evaluation of Precurso... (see metadata) ( )

msa : Multiple Sequence Alignment ( )

multiClust : multiClust: An R-package for Ide... (see metadata) ( )

multiMiR : Integration of multiple microRNA... (see metadata) ( )

multiscan : R package for combining multiple scans ( )

multtest : Resampling-based multiple hypothesis testing ( )

muscle : Multiple Sequence Alignment with MUSCLE ( )

mzID : An mzIdentML parser for R ( )

mzR : parser for netCDF, mzXML, mzData... (see metadata) ( )

ncdfFlow : ncdfFlow: A package that provide... (see metadata) ( )

ndexr : NDEx R client library ( )

nem : (Dynamic) Nested Effects Models ... (see metadata) ( )

netReg : Network-Regularized Regression Models ( )

netbiov : A package for visualizing comple... (see metadata) ( )

netprioR : A model for network-based prioritisation of genes ( )

netresponse : Functional Network Analysis ( )

networkBMA : Regression-based network inferen... (see metadata) ( )

nnNorm : Spatial and intensity based norm... (see metadata) ( )

nondetects : Non-detects in qPCR data ( )

normalize450K : Preprocessing of Illumina Infinium 450K data ( )

npGSEA : Permutation approximation method... (see metadata) ( )

nuCpos : An R package for prediction of n... (see metadata) ( )

nucleoSim : Generate synthetic nucleosome maps ( )

occugene : Functions for Multinomial Occupancy Distribution ( )

odseq : Outlier detection in multiple sequence alignments ( )

oligo : Preprocessing tools for oligonucleotide arrays ( )

omicade4 : Multiple co-inertia analysis of omics datasets ( )

onlineFDR : Online FDR control ( )

ontoProc : processing of ontologies of anat... (see metadata) ( )

oppar : Outlier profile and pathway analysis in R ( )

paircompviz : Multiple comparison test visualization ( )

pandaR : PANDA Algorithm ( )

panp : Presence-Absence Calls from Nega... (see metadata) ( )

parglms : support for parallelized estimation of GLMs/GEEs ( )

parody : Parametric And Resistant Outlier DYtection ( )

pathVar : Methods to Find Pathways with Si... (see metadata) ( )

pathifier : Quantify deregulation of pathways in cancer ( )

pathprint : Pathway fingerprinting for analy... (see metadata) ( )

pathwayPCA : Integrative Pathway Analysis wit... (see metadata) ( )

paxtoolsr : PaxtoolsR: Access Pathways from ... (see metadata) ( )

pcaGoPromoter : pcaGoPromoter is used to analyze... (see metadata) ( )

pcot2 : Principal Coordinates and Hotell... (see metadata) ( )

pdInfoBuilder : Platform Design Information Package Builder ( )

pepXMLTab : Parsing pepXML files and filter ... (see metadata) ( )

perturbatr : Statistical Analysis of High-Thr... (see metadata) ( )

pgca : PGCA: An Algorithm to Link Prote... (see metadata) ( )

philr : Phylogenetic partitioning based ... (see metadata) ( )

phosphonormalizer : Compensates for the bias introdu... (see metadata) ( )

phyloseq : Handling and analysis of high-th... (see metadata) ( )

piano : Platform for integrative analysis of omics data ( )

pickgene : Adaptive Gene Picking for Microa... (see metadata) ( )

pint : Pairwise INTegration of functional genomics data ( )

pkgDepTools : Package Dependency Tools ( )

plethy : R framework for exploration and ... (see metadata) ( )

plgem : Detect differential expression i... (see metadata) ( )

plier : Implements the Affymetrix PLIER algorithm ( )

plotGrouper : Shiny app GUI wrapper for ggplot... (see metadata) ( )

plrs : Piecewise Linear Regression Spli... (see metadata) ( )

plw : Probe level Locally moderated Weighted t-tests. ( )

pmm : Parallel Mixed Model ( )

pogos : PharmacOGenomics Ontology Support ( )

polyester : Simulate RNA-seq reads ( )

powerTCR : Model-Based Comparative Analysis... (see metadata) ( )

prada : Data analysis for cell-based functional assays ( )

predictionet : Inference for predictive network... (see metadata) ( )

preprocessCore : A collection of pre-processing functions ( )

procoil : Prediction of Oligomerization of... (see metadata) ( )

profileScoreDist : Profile score distributions ( )

progeny : Pathway RespOnsive GENes for act... (see metadata) ( )

proteinProfiles : Protein Profiling ( )

puma : Propagating Uncertainty in Micro... (see metadata) ( )

pvac : PCA-based gene filtering for Affymetrix arrays ( )

pvca : Principal Variance Component Analysis (PVCA) ( )

qckitfastq : FASTQ Quality Control ( )

qcmetrics : A Framework for Quality Control ( )

qpcrNorm : Data-driven normalization strate... (see metadata) ( )

quantsmooth : Quantile smoothing and genomic v... (see metadata) ( )

qusage : qusage: Quantitative Set Analysi... (see metadata) ( )

qvalue : Q-value estimation for false dis... (see metadata) ( )

rBiopaxParser : Parses BioPax files and represents them in R ( )

rDGIdb : R Wrapper for DGIdb ( )

rHVDM : Hidden Variable Dynamic Modeling ( )

rMAT : R implementation from MAT progra... (see metadata) ( )

rRDP : Interface to the RDP Classifier ( )

rTRM : Identification of transcriptiona... (see metadata) ( )

rWikiPathways : rWikiPathways - R client library... (see metadata) ( )

rain : Rhythmicity Analysis Incorporati... (see metadata) ( )

rama : Robust Analysis of MicroArrays ( )

randPack : Randomization routines for Clinical Trials ( )

rbsurv : Robust likelihood-based survival... (see metadata) ( )

reb : Regional Expression Biases ( )

rhdf5 : R Interface to HDF5 ( )

rhdf5client : Access HDF5 content from h5serv ( )

rmelting : R Interface to MELTING 5 ( )

rnaseqcomp : Benchmarks for RNA-seq Quantification Pipelines ( )

rols : An R interface to the Ontology Lookup Service ( )

ropls : PCA, PLS(-DA) and OPLS(-DA) for ... (see metadata) ( )

rpx : R Interface to the ProteomeXchange Repository ( )

rqubic : Qualitative biclustering algorit... (see metadata) ( )

sRAP : Simplified RNA-Seq Analysis Pipeline ( )

sSeq : Shrinkage estimation of dispersi... (see metadata) ( )

safe : Significance Analysis of Function and Expression ( )

sagenhaft : Collection of functions for read... (see metadata) ( )

sampleClassifier : Sample Classifier ( )

sangerseqR : Tools for Sanger Sequencing Data in R ( )

savR : Parse and analyze Illumina SAV files ( )

scFeatureFilter : A correlation-based method for q... (see metadata) ( )

scRecover : scRecover for imputation of sing... (see metadata) ( )

scsR : SiRNA correction for seed mediat... (see metadata) ( )

semisup : Semi-Supervised Mixture Model ( )

seqLogo : Sequence logos for DNA sequence alignments ( )

seqTools : Analysis of nucleotide, sequence... (see metadata) ( )

seqcombo : Visualization Tool for Sequence ... (see metadata) ( )

sevenbridges : Seven Bridges Platform API Clien... (see metadata) ( )

sigPathway : Pathway Analysis ( )

sigaR : Statistics for Integrative Genomics Analyses in R ( )

siggenes : Multiple Testing using SAM and E... (see metadata) ( )

sights : Statistics and dIagnostic Graphs for HTS ( )

signet : signet: Selection Inference in Gene NETworks ( )

sigsquared : Gene signature generation for fu... (see metadata) ( )

similaRpeak : Metrics to estimate a level of s... (see metadata) ( )

simpleaffy : Very simple high level analysis of Affymetrix data ( )

sincell : R package for the statistical as... (see metadata) ( )

sitePath : Detection of sites with fixation... (see metadata) ( )

sizepower : Sample Size and Power Calculatio... (see metadata) ( )

snapCGH : Segmentation, normalisation and ... (see metadata) ( )

snm : Supervised Normalization of Microarrays ( )

snpStats : SnpMatrix and XSnpMatrix classes and methods ( )

sparseDOSSA : Sparse Data Observations for Sim... (see metadata) ( )

specL : specL - Prepare Peptide Spectrum... (see metadata) ( )

spikeLI : Affymetrix Spike-in Langmuir Iso... (see metadata) ( )

spkTools : Methods for Spike-in Arrays ( )

splicegear : splicegear ( )

splots : Visualization of high-throughput... (see metadata) ( )

spotSegmentation : Microarray Spot Segmentation and... (see metadata) ( )

sscore : S-Score Algorithm for Affymetrix... (see metadata) ( )

sscu : Strength of Selected Codon Usage ( )

ssize : Estimate Microarray Sample Size ( )

ssrch : a simple search engine ( )

staRank : Stability Ranking ( )

statTarget : Statistical Analysis of Molecular Profiles ( )

stepNorm : Stepwise normalization functions... (see metadata) ( )

subSeq : Subsampling of high-throughput s... (see metadata) ( )

supraHex : supraHex: a supra-hexagonal map ... (see metadata) ( )

survcomp : Performance Assessment and Compa... (see metadata) ( )

sva : Surrogate Variable Analysis ( )

swfdr : Science-wise false discovery rat... (see metadata) ( )

switchBox : Utilities to train and validate ... (see metadata) ( )

synergyfinder : Calculate and Visualize Synergy ... (see metadata) ( )

synlet : Hits Selection for Synthetic Let... (see metadata) ( )

ternarynet : Ternary Network Estimation ( )

tigre : Transcription factor Inference t... (see metadata) ( )

tilingArray : Transcript mapping with high-den... (see metadata) ( )

timecourse : Statistical Analysis for Develop... (see metadata) ( )

timescape : Patient Clonal Timescapes ( )

tkWidgets : R based tk widgets ( )

topconfects : Top Confident Effect Sizes ( )

treeio : Base Classes and Functions for P... (see metadata) ( )

triform : Triform finds enriched regions (... (see metadata) ( )

trigger : Transcriptional Regulatory Infer... (see metadata) ( )

trio : Testing of SNPs and SNP Interact... (see metadata) ( )

tspair : Top Scoring Pairs for Microarray Classification ( )

tweeDEseq : RNA-seq data analysis using the ... (see metadata) ( )

twilight : Estimation of local false discovery rate ( )

twoddpcr : Classify 2-d Droplet Digital PCR... (see metadata) ( )

tximport : Import and summarize transcript-... (see metadata) ( )

unifiedWMWqPCR : Unified Wilcoxon-Mann Whitney Te... (see metadata) ( )

universalmotif : Import, Modify, and Export Motifs with R ( )

variancePartition : Quantify and interpret divers of... (see metadata) ( )

vbmp : Variational Bayesian Multinomial Probit Regression ( )

viper : Virtual Inference of Protein-act... (see metadata) ( )

vsn : Variance stabilization and calib... (see metadata) ( )

weaver : Tools and extensions for process... (see metadata) ( )

widgetTools : Creates an interactive tcltk widget ( )

xmapbridge : Export plotting files to the xma... (see metadata) ( )

xps : Processing and Analysis of Affym... (see metadata) ( )

yaqcaffy : Affymetrix expression data quali... (see metadata) ( )

zlibbioc : An R packaged zlib-1.2.5 ( )

Add an ebuild in portage :

The ebuild is now in the portage tree.

You can also use layman : emerge layman then layman -a R_Overlay

For Paludis use this rsync : rsync://gentoo.zugaina.org/R_Overlay-portage

If you have a problem : ycarus(-at-)zugaina.org