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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) ( )
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 ( )
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 ( )
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) ( )
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 ( )
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) ( )
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. ( )
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) ( )
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) ( )
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 ( )
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) ( )
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 :
- create the directory /usr/local/portage
- add in the file "make.conf" this : PORTDIR_OVERLAY="/usr/local/portage"
- create in the directory /usr/local/portage a sub-directory for the category, for example games-misc if you choose fortune-mod-french-0.02
- create an other sub-directory with the name of the ebuild (without the version number) for example fortune-mod-french
- copy or download the ebuild in this new directory (and if needed the other files in the sub-directory "files")
- Enter this command : ebuild lenomdelebuild.ebuild manifest, for example : ebuild fortune-mod-french-0.02.ebuild manifest
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