[Bioc-devel] recommend biocViews
Sonali Arora
sarora at fhcrc.org
Thu Jun 5 02:27:29 CEST 2014
Hi Everyone,
We have come up with a new function called "recommendBiocViews" which will
recommend biocViews to package Contributors by parsing the DESCRIPTION
file,
man page and vignettes of their package.
We also ran this function on all the "Software" packages in Rpacks(devel
branch)
to recommend additional biocViews for existing packages.
You can find the results in the attached file.
A small demo using the package "RefNet"
> data <- read.delim("recommendbiocViews.txt", row.names=1)
> data["RefNet",]
current recommended remove
RefNet GraphAndNetwork ThirdPartyClient, DataImport
It returns 4 columns:
column1 - current - existing biocViews which are present in ReferNet's
DESCRIPTION file
column2 - recommended - recommended biocViews which you can add in
addition to
existing biocViews (This is a recommended list - Please go through this
list and
find which biocViews best describe your package)
column3 - remove - existing biocViews which are inconsistent with current
Bioconductor biocViews
( Hint - you have a biocView which is discontinued, its spelling has
changed
( pay attention to cases, plural etc) )
Please remember that adding terms which are not part of the Bioconductor
biocViews will not lead to any additional visibility of your package.
Also misspelled biocViews in your package will lead to 'no-show' of your
package on the biocViews page.
eg: If you have 'CopyNumberVariations' in your DESCRIPTION file - your
package will not show up under 'CopyNumberVariation'
For a new package that you're developing, Please use BiocViews(Version:
1.33.4)
> library(BiocViews)
> recommendedBiocViews("packageDirectory")
A similar 3 column list is returned by parsing your package.
If you feel that these biocViews are appropriately recommended for your
package,
Please add them to your package.
--
Thanks and Regards,
Sonali.
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Package current recommended remove
multtest "Microarray, DifferentialExpression, MultipleComparison" "GeneExpression, Genetics, Regression, Survival"
ctc "Microarray, Clustering, Classification, DataImport, Visualization"
ROC DifferentialExpression Classification
tkWidgets Infrastructure
affyio "Microarray, DataImport, Infrastructure"
preprocessCore Infrastructure Preprocessing
affy "Microarray, OneChannel, Preprocessing"
vsn "Microarray, OneChannel, TwoChannel, Preprocessing" Normalization
makecdfenv "OneChannel, DataImport, Preprocessing" "Microarray, ChipOnChip"
widgetTools Infrastructure
Rgraphviz "GraphAndNetwork, Visualization"
affycomp "OneChannel, Microarray, Preprocessing"
limma "Microarray, OneChannel, TwoChannel, DataImport, QualityControl, Preprocessing, DifferentialExpression, MultipleComparison, TimeCourse" "GeneExpression, Genetics, Normalization, Bayesian, RNASeq"
splicegear "Infrastructure, Transcription" AlternativeSplicing
gcrma "Microarray, OneChannel, Preprocessing"
siggenes "MultipleComparison, Microarray, GeneExpression, SNP, ExonArray, DifferentialExpression" "mRNAMicroarray, Regression"
annaffy "OneChannel, Microarray, Annotation, GO, Pathways, ReportWriting"
daMA "Microarray, TwoChannel, DifferentialExpression" ExperimentalDesign
MeasurementError.cor StatisticalMethod "Microarray, mRNAMicroarray"
factDesign "Microarray, DifferentialExpression"
affyPLM "Microarray, OneChannel, Preprocessing, QualityControl" Normalization
webbioc "Infrastructure, Microarray, OneChannel, DifferentialExpression" "Preprocessing, TwoChannel, MultipleComparison, ReportWriting"
ecolitk "Annotation, Visualization" Sequencing
affypdnn "OneChannel, Microarray, Preprocessing" ChipOnChip
simpleaffy "Microarray, OneChannel, QualityControl, Preprocessing, Transcription, DataImport, DifferentialExpression, Annotation, ReportWriting, Visualization"
LPE "Microarray, DifferentialExpression" GeneExpression
pickgene "Microarray, DifferentialExpression" GeneExpression
Biostrings "SequenceMatching, Genetics, Sequencing, Infrastructure, DataImport, DataRepresentation"
qvalue MultipleComparison "GeneExpression, Preprocessing"
impute Microarray "GeneExpression, Clustering"
rama "Microarray, TwoChannel, QualityControl, Preprocessing" Bayesian
EBarrays "Clustering, DifferentialExpression" "GeneExpression, Microarray"
PROcess "MassSpectrometry, Proteomics"
altcdfenvs "Microarray, OneChannel, QualityControl, Preprocessing, Annotation, ProprietaryPlatforms, Transcription" "Sequencing, Genetics, SequenceMatching, GraphAndNetwork, DataImport"
arrayQuality "Microarray, TwoChannel, QualityControl, Visualization"
goTools "Microarray, GO, Visualization"
affylmGUI "Microarray, OneChannel, DataImport, QualityControl, Preprocessing, DifferentialExpression, MultipleComparison, GUI" "mRNAMicroarray, TwoChannel, TimeCourse"
limmaGUI "Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, DifferentialExpression, MultipleComparison, GUI" "OneChannel, TimeCourse"
marray "Microarray, TwoChannel, Preprocessing" "GeneExpression, Normalization, OneChannel, MultipleComparison, QualityControl, TimeCourse"
convert "Infrastructure, Microarray, TwoChannel" "GeneExpression, OneChannel, GeneTarget, Preprocessing, MultipleComparison, QualityControl, TimeCourse"
Resourcerer "Annotation, Microarray"
prada "CellBasedAssays, Visualization"
DNAcopy "Microarray, CopyNumberVariation"
aCGH "CopyNumberVariation, DataImport, Genetics" "Microarray, DifferentialExpression, MultipleComparison"
HEM "Microarray, DifferentialExpression"
GraphAT "Network, GraphAndNetwork" "Microarray, CellBiology"
MergeMaid "Microarray, DifferentialExpression, Visualization" "GeneExpression, Regression, Survival"
globaltest "Microarray, OneChannel, DifferentialExpression, GO, Pathways" "GeneExpression, GeneSetEnrichment"
OLIN "Microarray, TwoChannel, QualityControl, Preprocessing, Visualization" "OneChannel, mRNAMicroarray, Regression"
MLInterfaces "Classification, Clustering" Microarray
nnNorm "Microarray, TwoChannel, Preprocessing" Normalization
genArise "Microarray, TwoChannel, Preprocessing"
GLAD "Microarray, CopyNumberVariation"
twilight "Microarray, DifferentialExpression, MultipleComparison" GeneExpression
hopach Clustering GeneExpression
OLINgui "Microarray, TwoChannel, QualityControl, Preprocessing, Visualization" Normalization
DEDS "Microarray, DifferentialExpression" "GeneExpression, Preprocessing"
stepNorm "Microarray, TwoChannel, Preprocessing" Normalization
MVCClass "Visualization, Infrastructure, GraphAndNetwork"
macat "Microarray, DifferentialExpression, Visualization" "GeneExpression, ChipOnChip, Pathways"
SBMLR "GraphAndNetwork, Pathways, Network" SystemsBiology
sagenhaft SAGE "GeneExpression, Sequencing"
apComplex "NetworkInference, MassSpectrometry, GraphAndNetwork" Network
plier Software "Normalization, Preprocessing"
biomaRt Annotation
made4 "Clustering, Classification, MultipleComparison" "GeneExpression, Microarray"
spotSegmentation "Microarray, TwoChannel, QualityControl, Preprocessing" Clustering
tilingArray "Microarray, OneChannel, Preprocessing, Visualization"
safe "GeneExpression, FunctionalAnnotation" DifferentialExpression FunctionalAnnotation
plgem "Microarray, DifferentialExpression, Proteomics" GeneExpression
RankProd DifferentialExpression "GeneExpression, Microarray, GeneSignaling"
xcms "MassSpectrometry, Metabolomics" "Proteomics, DataImport"
MiPP "Microarray, Classification" "GeneExpression, Clustering"
idiogram Visualization Pathways
geneRecommender "Microarray, Clustering" GeneExpression
ssize "Microarray, DifferentialExpression" GeneExpression
bridge "Microarray, OneChannel, TwoChannel, DifferentialExpression" "GeneExpression, BatchEffect, Preprocessing, Bayesian, QualityControl"
oligo "Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, ExonArray, GeneExpression, DataImport" "Sequencing, Genetics, SequenceMatching"
clusterStab Clustering Microarray
pdmclass Classification "Microarray, Regression"
affyQCReport "Microarray, OneChannel, QualityControl" Preprocessing
fdrame "Microarray, DifferentialExpression, MultipleComparison" ExperimentalDesign
LMGene "Microarray, DifferentialExpression, Preprocessing" "GeneExpression, Genetics, ExperimentalDesign, MultipleComparison, Normalization, OneChannel"
diffGeneAnalysis "Microarray, DifferentialExpression" "GeneExpression, Normalization"
timecourse "Microarray, TimeCourse, DifferentialExpression"
reb "Microarray, CopyNumberVariation, Visualization"
maanova "Microarray, DifferentialExpression, Clustering"
affxparser "Infrastructure, DataImport" "ChipOnChip, QualityControl"
GlobalAncova "Microarray, OneChannel, DifferentialExpression, Pathways" "GeneExpression, TissueMicroarray"
maSigPro "Microarray, DifferentialExpression, TimeCourse" "GeneExpression, Regression"
RLMM "Microarray, OneChannel, SNP, GeneticVariability" "ChipOnChip, Classification"
affycoretools "ReportWriting, Microarray, OneChannel, GeneExpression" Preprocessing
MANOR "Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, CopyNumberVariation" Normalization
MantelCorr Clustering "GeneExpression, Microarray"
panp Infrastructure "GeneExpression, Microarray, ChipOnChip, Preprocessing, OneChannel"
pathRender "GraphAndNetwork, Pathways, Visualization"
GEOquery "Microarray, DataImport, OneChannel, TwoChannel, SAGE" GeneExpression
codelink "Microarray, OneChannel, DataImport, Preprocessing" "TwoChannel, MultipleComparison, QualityControl, TimeCourse"
metaArray "Microarray, DifferentialExpression" GeneExpression
snapCGH "Microarray, CopyNumberVariation, TwoChannel, Preprocessing" "GeneExpression, GeneTarget, OneChannel, MultipleComparison, QualityControl, TimeCourse"
sscore DifferentialExpression "Microarray, Preprocessing, OneChannel, DataImport"
ScISI "GraphAndNetwork, Proteomics, NetworkInference, DecisionTree" "Pathways, MassSpectrometry"
beadarray "Microarray, OneChannel, QualityControl, Preprocessing"
Mfuzz "Microarray, Clustering, TimeCourse, Preprocessing, Visualization" GeneExpression
adSplit "Microarray, Clustering" GeneExpression
copa "OneChannel, TwoChannel, DifferentialExpression, Visualization" Transcription
sizepower Microarray "GeneExpression, ExperimentalDesign"
SNPchip "CopyNumberVariation, SNP, GeneticVariability, Visualization"
cellHTS "CellBasedAssays, Visualization"
EBImage Visualization
OCplus "Microarray, DifferentialExpression, MultipleComparison"
Heatplus "Microarray, Visualization" Clustering
maCorrPlot "Microarray, Preprocessing, Visualization" "GeneExpression, Normalization"
nudge "Microarray, TwoChannel, DifferentialExpression" "GeneExpression, mRNAMicroarray"
cghMCR "Microarray, CopyNumberVariation" "Preprocessing, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse"
OrderedList "Microarray, DifferentialExpression, MultipleComparison" GeneExpression
logicFS "SNP, Classification, Genetics" Regression
BSgenome "Genetics, Infrastructure, DataRepresentation, SequenceMatching, Annotation, SNP" "Sequencing, Coverage, GenomeAssembly, GenomeAnnotation"
TypeInfo Infrastructure TimeCourse
gaggle "ThirdPartyClient, Visualization, Annotation, GraphAndNetwork, DataImport" Network
sigPathway "DifferentialExpression, MultipleComparison" GeneExpression
ABarray "Microarray, OneChannel, Preprocessing" "GeneExpression, mRNAMicroarray, TissueMicroarray, Normalization, Clustering"
Harshlight "Microarray, QualityControl, Preprocessing, OneChannel, ReportWriting" ChipOnChip
quantsmooth "Visualization, CopyNumberVariation" Genetics
aroma.light "Infrastructure, Microarray, OneChannel, TwoChannel, MultiChannel, Visualization, Preprocessing" "GeneExpression, mRNAMicroarray, Normalization"
pcot2 "Microarray, DifferentialExpression" "GeneExpression, Network"
spikeLI "Microarray, QualityControl"
BioMVCClass "Visualization, Infrastructure, GraphAndNetwork"
lapmix "Microarray, OneChannel, DifferentialExpression" Bayesian
GGtools "Genetics, GeneExpression, GeneticVariability, SNP" "GenePrediction, GenomeAnnotation, VariantAnnotation"
beadarraySNP "CopyNumberVariation, SNP, GeneticVariability, TwoChannel, Preprocessing, DataImport" Normalization
pkgDepTools "Infrastructure, GraphAndNetwork" Network
splots "Visualization, Sequencing, MicrotitrePlateAssay"
SAGx "Microarray, OneChannel, Preprocessing, DataImport, DifferentialExpression, Clustering, MultipleComparison" "GeneExpression, GeneSetEnrichment, Pathways, Regression"
nem "Microarray, GraphAndNetwork, Pathways, DecisionTree" "Preprocessing, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse"
pcaMethods Bayesian
RbcBook1 Software GraphAndNetwork
flowCore "Infrastructure, FlowCytometry, CellBasedAssays"
flowUtils "Infrastructure, FlowCytometry, CellBasedAssays, DecisionTree" DataImport
flowQ "Infrastructure, FlowCytometry, CellBasedAssays" "QualityControl, MultipleComparison"
flowViz "Infrastructure, Flowcytometry, CellBasedAssays, Visualization" FlowCytometry Flowcytometry
RefPlus "Microarray, OneChannel, Preprocessing" QualityControl
occugene "Annotation, Pathways" GenomeAnnotation
lumi "Microarray, OneChannel, Preprocessing, DNAMethylation, QualityControl, TwoChannel" "GeneExpression, MethylationArray, Normalization"
pdInfoBuilder "Annotation, Infrastructure" "ChipOnChip, GenomeAnnotation, BiocViews"
BufferedMatrix Infrastructure
BufferedMatrixMethods Infrastructure Microarray
GeneticsDesign Genetics
seqLogo SequenceMatching
topGO "Microarray, Visualization" "GeneSetEnrichment, GraphAndNetwork"
annotationTools "Microarray, Annotation" GeneExpression
LBE MultipleComparison "GeneExpression, GenePrediction, Classification"
SLqPCR "MicrotitrePlateAssay, qPCR" "GeneExpression, Normalization"
rHVDM "Microarray, GraphAndNetwork, Transcription, Classification, NetworkInference" "Preprocessing, OneChannel"
CALIB "Microarray, TwoChannel, Preprocessing" "OneChannel, MultipleComparison, QualityControl, TimeCourse"
PGSEA Microarray "GeneExpression, GeneSetEnrichment, OneChannel, ReportWriting"
Ringo "Microarray, TwoChannel, DataImport, QualityControl, Preprocessing" "OneChannel, MultipleComparison, TimeCourse"
ACME "Technology, Microarray, Normalization" GenomeAnnotation
RWebServices Infrastructure
MassSpecWavelet "MassSpectrometry, Proteomics"
GeneticsPed Genetics
CORREP "Microarray, Clustering, GraphAndNetwork" GeneExpression
oneChannelGUI "Sequencing, RNASeq, Microarray, OneChannel, DataImport, QualityControl, Preprocessing, StatisticalMethod, DifferentialExpression, GUI, MultipleComparison" "Coverage, ExonArray, GeneExpression"
rbsurv Microarray "GeneExpression, Survival"
bgx "Microarray, DifferentialExpression" "GeneExpression, Preprocessing, Bayesian, OneChannel"
puma "Microarray, OneChannel, Preprocessing, Bioinformatics, DifferentialExpression, Clustering" "ExonArray, GeneExpression, mRNAMicroarray, ChipOnChip, AlternativeSplicing, DifferentialSplicing, Bayesian, TwoChannel, DataImport" Bioinformatics
cellHTS2 "CellBasedAssays, Preprocessing, Visualization" "Sequencing, Microarray, CellBiology, GeneTarget, GenomeAnnotation, DataImport, OneChannel, TwoChannel, MicrotitrePlateAssay"
biocGraph "Visualization, GraphAndNetwork"
keggorthology "Pathways, GraphAndNetwork, Visualization" GenomeAnnotation
SMAP "Microarray, TwoChannel, CopyNumberVariation"
explorase "Visualization, Microarray, GUI" "SystemsBiology, ExperimentalDesign"
vbmp Classification "GeneExpression, GenePrediction, GeneTarget, Bayesian, Regression"
arrayQualityMetrics "Microarray, QualityControl, OneChannel, TwoChannel, ReportWriting"
CGHcall "Microarray, Preprocessing, Visualization" CopyNumberVariation
AffyExpress "Microarray, OneChannel, QualityControl, Preprocessing, DifferentialExpression, Annotation, ReportWriting, Visualization" "GeneExpression, MultipleComparison, Regression, TwoChannel, TimeCourse"
oligoClasses Infrastructure
VanillaICE CopyNumberVariants "GenomeAnnotation, HiddenMarkovModel" CopyNumberVariants
OutlierD Microarray Regression
bgafun Classification Alignment
rsbml "GraphAndNetwork, Pathways, Network" SystemsBiology
maigesPack "Microarray, TwoChannel, Preprocessing, ThirdPartyClient, DifferentialExpression, Clustering, Classification, GraphAndNetwork" "GeneExpression, TissueMicroarray, Genetics, Pathways, OneChannel, MultipleComparison, QualityControl, TimeCourse"
yaqcaffy "Microarray, OneChannel, QualityControl, ReportWriting" "Transcription, WholeGenome, DifferentialExpression, DataImport"
Rdisop MassSpectrometry
xps "ExonArray, GeneExpression, Microarray, OneChannel, DataImport, Preprocessing, Transcription, DifferentialExpression" "WholeGenome, GenomeAnnotation"
Rtreemix StatisctialMethod Pathways StatisctialMethod
BGmix "Microarray, DifferentialExpression, MultipleComparison" "GeneExpression, Bayesian"
plw "Microarray, OneChannel, TwoChannel, DifferentialExpression" Preprocessing
gaga "OneChannel, MassSpectrometry, MultipleComparison, DifferentialExpression, Classification" "GeneExpression, Clustering, PatternLogic"
SLGI "GraphAndNetwork, Proteomics, Genetics, Network" "NetworkInference, DecisionTree"
PCpheno "GraphAndNetwork, Proteomics, Network" "Genetics, Pathways, GeneSetEnrichment, NetworkInference, DecisionTree"
BAC "Microarray, Transcription" Bayesian
XDE "Microarray, DifferentialExpression" "GeneExpression, Bayesian"
GraphAlignment "GraphAndNetwork, Network" "Alignment, Bayesian"
mdqc "Microarray, QualityControl" "GeneExpression, Classification"
BCRANK "MotifDiscovery, GeneRegulation" Transcription
snpStats "Microarray, SNP, GeneticVariability"
GSEAlm Microarray "GeneExpression, GeneSetEnrichment, Regression"
affyPara "Microarray, Preprocessing" "OneChannel, TwoChannel, DataImport"
flowClust "Clustering, Visualization, FlowCytometry" "Network, CellBasedAssays, GraphAndNetwork"
GeneSelector "StatisticalMethod, DifferentialExpression"
GEOmetadb Infrastructure "GeneExpression, Microarray, OneChannel, TwoChannel, DataImport"
GenomeGraphs "Visualization, Microarray" "Sequencing, GenomeAnnotation"
RBioinf "GeneExpression, Microarray, Preprocessing, QualityControl, Classification, Clustering, MultipleComparison, Annotation" GraphAndNetwork
rtracklayer "Annotation, Visualization, DataImport" "Genetics, GenomeAnnotation, GenomeBrowsers"
GGBase "Genetics, Infrastructure" "GeneExpression, Microarray, mRNAMicroarray, Bayesian, Regression, GeneticVariability"
AffyCompatible "Infrastructure, Microarray, OneChannel"
goProfiles "Microarray, GO"
LPEadj "Microarray, Proteomics" "GeneExpression, DifferentialExpression"
CGHbase "Infrastructure, Microarray, CopyNumberVariation" "Preprocessing, TwoChannel"
CGHregions "Microarray, CopyNumberVariation, Visualization" "Clustering, DimensionReduction"
CMA "Classification, DecisionTree"
HELP "CpGIsland, DNAMethylation, Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, Visualization"
SIM "Microarray, Visualization"
miRNApath "Annotation, Pathways, DifferentialExpression, NetworkEnrichment, miRNA"
multiscan "Microarray, Preprocessing" "GeneExpression, OneChannel, TwoChannel, mRNAMicroarray, Regression"
minet "Microarray, GraphAndNetwork, Network, NetworkInference"
iterativeBMA "Microarray, Classification" Bayesian
ITALICS "Microarray, CopyNumberVariation" "Preprocessing, ExonArray, GeneExpression, OneChannel, TwoChannel, DifferentialExpression, DataImport"
iterativeBMAsurv Microarray "GeneExpression, mRNAMicroarray, Bayesian, Classification, Regression, Survival"
DFP "Microarray, DifferentialExpression" GeneExpression
domainsignatures "Annotation, Pathways, GeneSetEnrichment" CellBasedAssays
RpsiXML "Infrastructure, Proteomics" "Pathways, Network, GraphAndNetwork"
logitT "Microarray, DifferentialExpression" "GeneExpression, mRNAMicroarray, ChipOnChip, ExperimentalDesign, Preprocessing, OneChannel"
PLPE "Proteomics, Microarray, DifferentialExpression" MassSpectrometry
edgeR "Bioinformatics, DifferentialExpression, SAGE, HighThroughputSequencing, RNAseq, ChIPseq" "GeneExpression, RNASeq, Microarray, mRNAMicroarray, Preprocessing, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse" "Bioinformatics, HighThroughputSequencing, RNAseq, ChIPseq"
MEDME "Microarray, CpGIsland, DNAMethylation"
ArrayTools "Microarray, OneChannel, QualityControl, Preprocessing, StatisticalMethod, DifferentialExpression, Annotation, ReportWriting, Visualization" MultipleComparison
microRNA "Infrastructure, GenomeAnnotation, SequenceMatching"
RNAither "CellBasedAssays, QualityControl, Preprocessing, Visualization, Annotation, GO" "Microarray, Normalization, DifferentialExpression"
ArrayExpress "Microarray, DataImport, OneChannel, TwoChannel"
KCsmart "CopyNumberVariation, Visualization, aCGH, Microarray" "ExonArray, GeneExpression, DifferentialExpression, MultipleComparison"
ChemmineR "MicrotitrePlateAssay, CellBasedAssays, Visualization, Infrastructure, DataImport, Clustering, Bioinformatics, Proteomics" "Cheminformatics, Classification" Bioinformatics
parody MultipleComparison
xmapbridge "Annotation, ReportWriting, Visualization" "ExonArray, CellBiology, GeneTarget, GenomeAnnotation"
affyContam Infrastructure "Microarray, Preprocessing, OneChannel"
arrayMvout "Infrastructure, Microarray, QualityControl" "Preprocessing, OneChannel, MultipleComparison"
BicARE "Microarray, Transcription, Clustering" "BiocViews, DifferentialExpression, MultipleComparison"
HilbertVis Visualization
HilbertVisGUI Visualization
flagme "DifferentialExpression, MassSpectrometry" "Metabolomics, PeakDetection"
MCRestimate Classification Preprocessing
AffyTiling "Microarray, Preprocessing" Normalization
GOSemSim "GO, Clustering, Pathways, Network"
KEGGgraph "Pathways, GraphAndNetwork, Visualization"
qpgraph "Microarray, GeneExpression, Transcription, Pathways, NetworkInference, GraphAndNetwork, GeneRegulation" "mRNAMicroarray, GeneTarget, Network"
spkTools "Software, Technology, Microarray"
tspair Microarray "GeneExpression, Classification"
SPIA "Microarray, GraphAndNetwork" "GeneExpression, TissueMicroarray, GeneSignaling, Pathways"
DAVIDQuery Annotation
metahdep "Microarray, DifferentialExpression" "GeneExpression, ChipOnChip"
CAMERA MassSpectrometry Metabolomics
genomeIntervals "DataImport, Infrastructure, Genetics"
PAnnBuilder "Annotation, Proteomics"
flowFlowJo FlowCytometry
GeneSelectMMD DifferentialExpression "Microarray, TissueMicroarray"
betr "Microarray, DifferentialExpression, TimeCourse" "Genetics, Bayesian"
crlmm "Microarray, Preprocessing, SNP, CopyNumberVariation"
dyebias "Microarray, TwoChannel, QualityControl, Preprocessing"
qpcrNorm "Preprocessing, GeneExpression" "Microarray, Normalization, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse"
SSPA "Microarray, StatisticalMethod" "Sequencing, Preprocessing, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse"
GeneRegionScan "Microarray, DataImport, SNP, OneChannel, Visualization" "Sequencing, Genetics, SequenceMatching"
rMAT "Microarray, Preprocessing" DataImport
flowStats "FlowCytometry, CellBasedAssays" "Preprocessing, DataImport"
TargetSearch "MassSpectrometry, Preprocessing, DecisionTree" "Proteomics, DataImport"
Rmagpie "Microarray, Classification"
SJava Infrastructure
methylumi "DNAMethylation, TwoChannel, Preprocessing, QualityControl, CpGIsland" DataImport
CNTools "Microarray, CopyNumberVariation" Classification
RmiR "Software, GeneExpression, Microarray, TimeCourse, Visualization"
flowMerge "Clustering, FlowCytometry" GraphAndNetwork
flowFP "FlowCytometry, CellBasedAssays, Clustering, Visualization"
BUS Preprocessing "Microarray, Network, NetworkInference, GraphAndNetwork"
Rolexa "Sequencing, DataImport, Preprocessing, QualityControl" "OneChannel, Normalization"
ddCt "GeneExpression, DifferentialExpression, MicrotitrePlateAssay, qPCR"
ChIPpeakAnno "Annotation, ChIPSeq, ChIPchip" "Transcription, Sequencing, Genetics, SequenceMatching, DataImport"
Starr "Microarray, OneChannel, DataImport, QualityControl, Preprocessing, ChIPchip" ChipOnChip
mBPCR "aCGH, SNP, Microarray, CopyNumberVariation" "WholeGenome, Bayesian, Regression, DataImport, GeneticVariability"
ChIPsim "Infrastructure, ChIPSeq" "Sequencing, Genetics, NucleosomePositioning, SequenceMatching, DataImport"
plateCore "FlowCytometry, Infrastructure, CellBasedAssays"
MiChip "Microarray, Preprocessing"
clippda "Proteomics, OneChannel, Preprocessing, DifferentialExpression, MultipleComparison, SampleSize" "Microarray, MassSpectrometry, TwoChannel, QualityControl, TimeCourse" SampleSize
AgiMicroRna "Microarray, AgilentChip, OneChannel, Preprocessing, DifferentialExpression" "GeneExpression, Genetics, GeneTarget, ExperimentalDesign, MultipleComparison, TwoChannel, QualityControl, ReportWriting, TimeCourse" AgilentChip
RTCA "CellBasedAssays, Infrastructure, Visualization, TimeCourse"
CGHnormaliter "Microarray, Preprocessing" "Normalization, CopyNumberVariation"
cycle "Microarray, TimeCourse" "GeneExpression, Preprocessing, Clustering"
baySeq "Bioinformatics, HighThroughputSequencing, DifferentialExpression, MultipleComparisons, SAGE" "Sequencing, Genetics, Coverage, Bayesian" "Bioinformatics, HighThroughputSequencing, MultipleComparisons"
GeneAnswers "Infrastructure, DataRepresentation, Visualization, GraphAndNetwork" Network
ChromHeatMap Visualization "GeneExpression, CellBiology, GenomeAnnotation, Pathways, Survival"
ChIPseqR "ChIPSeq, Infrastructure" "Sequencing, NucleosomePositioning, QualityControl, DataImport"
HTqPCR "MicrotitrePlateAssay, DifferentialExpression, GeneExpression, DataImport, QualityControl, Preprocessing, Visualization, MultipleComparison, qPCR" "Microarray, mRNAMicroarray, OneChannel, TwoChannel, TimeCourse"
CNVtools GeneticVariability
LiquidAssociation "Pathways, GeneExpression, CellBiology, Genetics, Network, TimeCourse"
BioSeqClass Classification RNASeq
DEGseq "RNASeq, Preprocessing, GeneExpression, DifferentialExpression" "Sequencing, RIPSeq, Microarray, mRNAMicroarray, GenomeAnnotation, Regression, MultipleComparison"
SpeCond "Microarray, DifferentialExpression, MultipleComparison, Clustering, ReportWriting" GeneExpression
Genominator Infrastructure "Sequencing, Microarray"
eisa "Classification, Visualization, Microarray, GeneExpression" Transcription
CSAR "ChIPSeq, Transcription, Genetics" "Sequencing, ChipOnChip, Coverage, Pathways"
DESeq "Sequencing, ChIPSeq, RNASeq, SAGE, DifferentialExpression" GeneExpression
frma "Software, Microarray, Preprocessing" GeneExpression
frmaTools "Software, Microarray, Preprocessing" OneChannel
hyperdraw "Visualization, GraphAndNetwork"
ConsensusClusterPlus "Software, Clustering" "GeneExpression, Microarray"
iChip "ChIPchip, NimbleGen, OneChannel, Agilent, Microarray" "GeneExpression, DifferentialExpression, Bayesian" "NimbleGen, Agilent"
rGADEM "Microarray, ChIPchip, Sequencing, ChIPSeq, GenomicSequence, MotifDiscovery" "Genetics, MotifAnnotation, SequenceMatching, DataImport" GenomicSequence
methVisual "DNAMethylation, Clustering, Classification" "Sequencing, Genetics, Alignment, SequenceMatching, DataImport"
pint "aCGH, GeneExpression, Genetics, DifferentialExpression, Microarray" "WholeGenome, FunctionalGenomics"
MassArray "DNAMethylation, SNP, MassSpectrometry, Genetics, DataImport, Visualization" QualityControl
charm "Microarray, DNAMethylation" MethylationArray
SamSPECTRAL "FlowCytometry, CellBiology, Clustering, Cancer, FlowCytometry, StemCells, HIV" "Cancer, StemCells, HIV"
segmentSeq "Bioinformatics, HighThroughputSequencing, MultipleComparisons" "Sequencing, Alignment, DifferentialExpression, QualityControl, DataImport" "Bioinformatics, HighThroughputSequencing, MultipleComparisons"
genoCN "Microarray, Genetics"
BeadDataPackR Microarray "OneChannel, TwoChannel"
MotIV "Microarray, ChIPchip, ChIPSeq, GenomicSequence, MotifAnnotation" Alignment GenomicSequence
girafe Sequencing "Coverage, Alignment, DataImport"
ExpressionView "Classification, Visualization, Microarray, GeneExpression" "GeneSetEnrichment, Normalization"
tigre "Microarray, TimeCourse, GeneExpression, Transcription, GeneRegulation, NetworkInference, Bayesian" "DifferentialExpression, GeneTarget"
goseq "Sequencing, GO, GeneExpression, Transcription, RNASeq" DifferentialExpression
BayesPeak ChIPSeq "Sequencing, RIPSeq, ChipOnChip, Bayesian, HiddenMarkovModel"
SRAdb "Infrastructure, Sequencing, DataImport" "Alignment, GraphAndNetwork"
PICS "Clustering, Visualization, Sequencing, ChIPSeq"
flowMeans "FlowCytometry, CellBiology, Clustering, Cancer, FlowCytometry, StemCells, HIV" Regression "Cancer, StemCells, HIV"
PROMISE "Microarray, OneChannel, MultipleComparison, GeneExpression"
GEOsubmission Microarray
GSRI "Microarray, Transcription, DifferentialExpression, Enrichment, GeneSetEnrichment" GeneRegulation Enrichment
flowTrans FlowCytometry "Clustering, CellBasedAssays"
genomes "Annotation, Genetics" "Sequencing, Coverage, GenomeAnnotation, SequenceMatching, DataImport"
affyILM "Microarray, OneChannel, Preprocessing" "GeneExpression, ChipOnChip, GeneTarget"
attract "StatisticalMethod, GeneExpression" "Microarray, GeneSetEnrichment, Pathways, Preprocessing, Clustering, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse"
fabia "StatisticalMethod, Microarray, DifferentialExpression, MultipleComparison, Clustering, Visualization" "GeneExpression, Bayesian"
BHC "Microarray, Clustering" "Bayesian, TimeCourse"
coRNAi CellBasedAssays "Microarray, Preprocessing, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse"
NTW Preprocessing "GeneExpression, DifferentialExpression, Network, Regression"
MBCB "Microarray, Preprocessing" Bayesian
IsoGeneGUI "Microarray, DifferentialExpression, GUI" "GeneExpression, Genetics, MultipleComparison, QualityControl"
CoGAPS "GeneExpression, Microarray"
BioNet "Microarray, DataImport, GraphAndNetwork, Network, NetworkEnrichment, GeneExpression, DifferentialExpression"
CGEN "SNP, MultipleComparison, Clustering" Regression
HTSanalyzeR "CellBasedAssays, MultipleComparison" "GeneSetEnrichment, NetworkEnrichment, Network"
imageHTS "Software, CellBasedAssays, Preprocessing, Visualization"
RDRToolbox "Dimension, DimensionReduction, FeatureExtraction, Visualization, Clustering, Microarray" GeneExpression Dimension
NuPoP "Genetics, Visualization, Classification" "NucleosomePositioning, HiddenMarkovModel"
RCytoscape "Visualization, GraphAndNetwork, ThirdPartyClient" Network
farms "GeneExpression, Microarray, Preprocessing, QualityControl" OneChannel
Mulcom "StatisticalMethod, MultipleComparison, Microarray, DifferentialExpression, GeneExpression"
les "Microarray, DifferentialExpression, ChIPchip, DNAMethylation, Transcription" Regression
SQUADD "GraphAndNetwork, Network, Visualization"
OTUbase "Sequencing, DataImport" QualityControl
netresponse "CellBiology, Clustering, GeneExpression, Genetics, Network, GraphAndNetwork, DifferentialExpression, Microarray, Transcription" "NetworkInference, MultipleComparison"
iSeq "ChIPSeq, Sequencing" "ChipOnChip, Bayesian"
LVSmiRNA "Microarray, AgilentChip, OneChannel, Preprocessing" Normalization AgilentChip
gage "Pathways, GO, DifferentialExpression, Microarray, OneChannel, TwoChannel, RNAseq, Genetics, MultipleComparisons, GeneSetEnrichment" MultipleComparison "RNAseq, MultipleComparisons"
CRImage "CellBiology, Classification" "Microarray, mRNAMicroarray, Genetics, CopyNumberVariation, DataImport"
ontoCAT "Classification, DataRepresentation"
rnaSeqMap "Annotation, ReportWriting, Transcription, GeneExpression, DifferentialExpression, Sequencing, RNASeq, SAGE, Visualization" "Genetics, Coverage, DataImport"
GeneGA GeneExpression
R453Plus1Toolbox "Sequencing, Infrastructure, DataImport, DataRepresentation, Visualization, QualityControl, ReportWriting" "Genetics, Coverage, GenomeAnnotation, Alignment, SequenceMatching"
ADaCGH2 "Microarray, CopyNumberVariation"
MEDIPS "DNAMethylation, CpGIsland, DifferentialExpression, Sequencing, ChIPSeq, Preprocessing, QualityControl, Visualization" "Microarray, Genetics, Coverage, GenomeAnnotation, CopyNumberVariation, SequenceMatching"
DEGraph "Microarray, DifferentialExpression, GraphAndNetwork, Network, NetworkEnrichment, DecisionTree" "GeneExpression, GeneSetEnrichment, Pathways"
MLP Genetics
phenoDist CellBasedAssays "Preprocessing, Clustering"
IPPD Proteomics MassSpectrometry
gaia "aCGH, CopyNumberVariation"
snm "Microarray, OneChannel, TwoChannel, MultiChannel, DifferentialExpression, ExonArray, GeneExpression, Transcription, MultipleComparison, Preprocessing, QualityControl" Normalization
TEQC "QualityControl, Microarray, Sequencing, Genetics" Coverage
flowPhyto "FlowCytometry, DataImport, QualityControl, Classification, Visualization, Clustering"
TurboNorm "Microarray, OneChannel, TwoChannel, Preprocessing, DNAMethylation, CpGIsland" "MethylationArray, Normalization, MultipleComparison, QualityControl, TimeCourse"
Vega "aCGH, CopyNumberVariation" "WholeGenome, Genetics"
Clonality "Microarray, CopyNumberVariation, Classification, aCGH"
mgsa "Pathways, GO, GeneSetEnrichment" Bayesian
seqbias Sequencing "Genetics, Coverage, GenomeAnnotation, Bayesian"
TDARACNE "Microarray, TimeCourse" "Network, GraphAndNetwork"
phenoTest "Microarray, DifferentialExpression, MultipleComparison, Clustering, Classification" "GeneExpression, GeneSetEnrichment, Pathways"
ExiMiR "Microarray, OneChannel, TwoChannel, Preprocessing, GeneExpression, Transcription" "Normalization, MultipleComparison, QualityControl, TimeCourse"
mosaics "ChIPSeq, Sequencing, Transcription, Genetics" ChipOnChip
chopsticks "Microarray, SNPsAndGeneticVariability, SNP, GeneticVariability" "WholeGenome, GenomeAnnotation" SNPsAndGeneticVariability
pvac "Microarray, OneChannel, QualityControl" "GeneExpression, GeneTarget"
joda "Microarray, Pathways, GraphAndNetwork, StatisticalMethod, NetworkInference" "GeneExpression, Transcription, GeneSignaling, Network"
procoil "Proteomics, Classification" "Normalization, SupportVectorMachine"
RNAinteract "CellBasedAssays, QualityControl, Preprocessing, Visualization"
clst Classification
clstutils "Sequencing, Classification, Visualization, QualityControl"
inveRsion "Microarray, SNP" Classification
clusterProfiler "Clustering, GO, Pathways, Visualization, MultipleComparison, GeneSetEnrichment"
MSnbase "Infrastructure, Proteomics, MassSpectrometry, QualityControl" DataImport
ibh "QualityControl, DataImport, GraphAndNetwork, NetworkEnrichment" "Network, Clustering"
flowPlots "FlowCytometry, CellBasedAssays, Visualization, DataRepresentation"
AnnotationFuncs "AnnotationData, Software" AnnotationData
ENVISIONQuery Annotation
cn.farms "Microarray, CopyNumberVariation"
mcaGUI "GUI, Visualization, Clustering, Sequencing" DataImport
Rsubread "Sequencing, Alignment, SequenceMatching, RNASeq, ChIPSeq, GeneExpression, GeneRegulation, Genetics, SNP, GeneticVariability, Preprocessing, QualityControl, GenomeAnnotation, Software" DNASeq
genefu "DifferentialExpression, GeneExpression, Visualization, Clustering, Classification" "Microarray, VariantAnnotation, Survival"
survcomp "GeneExpression, DifferentialExpression, Visualization" "Microarray, GenePrediction, GeneSignaling, Survival"
genoset "Infrastructure, DataRepresentation, Microarray, SNP, CopyNumberVariation"
qrqc "Sequencing, QualityControl, DataImport, Preprocessing, Visualization" "Genetics, SequenceMatching"
lol StatisticalMethod GenomeAnnotation
NCIgraph "Pathways, GraphAndNetwork"
a4Base Microarray "Preprocessing, OneChannel, TwoChannel, DifferentialExpression, MultipleComparison, QualityControl, ReportWriting, TimeCourse"
a4Preproc Microarray Preprocessing
a4Classif Microarray "GeneExpression, Classification, Clustering"
a4Core Microarray Classification
a4Reporting Microarray "OneChannel, ReportWriting"
a4 Microarray "GeneExpression, mRNAMicroarray, DifferentialExpression, FunctionalPrediction, GenePrediction, GeneTarget, Preprocessing, Classification, Clustering, Regression"
anota "GeneExpression, DifferentialExpression, Microarray, Sequencing" MultipleComparison
GSVA "Microarray, Pathways, GeneSetEnrichment" "GeneExpression, Survival"
ArrayExpressHTS "RNASeq, Sequencing" "Transcription, Coverage, DataImport"
flowWorkspace "FlowCytometry, DataImport, Preprocessing, DataRepresentation" CellBasedAssays
REDseq "Sequencing, SequenceMatching, Preprocessing" "RIPSeq, Microarray, Genetics, GenomeAnnotation, ChIPchip, ChIPSeq, DifferentialExpression, MultipleComparison, DataImport"
RCASPAR "aCGH, GeneExpression, Genetics, Proteomics, Visualization" "GenePrediction, Regression, Survival"
DOSE Annotation
DEXSeq "Sequencing, RNASeq, DifferentialExpression" "Genetics, Coverage, Normalization, ChIPSeq"
randPack StatisticalMethod
cqn "RNASeq, Preprocessing, DifferentialExpression" "Sequencing, Normalization"
inSilicoDb "Microarray, DataImport" ChipOnChip
Repitools "DNAMethylation, GeneExpression, MethylSeq" "DifferentialExpression, DifferentialMethylation"
flowType FlowCytometry OneChannel
ReadqPCR "DataImport, MicrotitrePlateAssay, GeneExpression, qPCR" "Microarray, Preprocessing, OneChannel"
Cormotif "Microarray, DifferentialExpression" "Preprocessing, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse"
GOFunction "GO, Pathways, Microarray, GeneSetEnrichment" "GeneExpression, GraphAndNetwork"
IdMappingRetrieval "Annotation, MultipleComparison"
GRENITS "NetworkInference, GeneRegulation, TimeCourse, GraphAndNetwork" "GeneExpression, Network, Bayesian"
htSeqTools "Sequencing, QualityControl" "ChipOnChip, Genetics, Coverage, RNASeq, SequenceMatching"
RamiGO "GO, Visualization, GraphAndNetwork, Classification, ThirdPartyClient" Network
RedeR "GraphsAndNetworks, NetworkVisualization, Networks, Software, Visualization" "GraphsAndNetworks, NetworkVisualization, Networks"
nucleR "ChIPSeq, Microarray, Sequencing, Genetics" "Coverage, NucleosomePositioning, QualityControl, DataImport"
NormqPCR "MicrotitrePlateAssay, GeneExpression, qPCR" "Transcription, Normalization, DataImport"
Streamer "Infrastructure, DataImport"
VariantAnnotation "DataImport, Sequencing, SNP, Annotation, Genetics, Homo_sapiens" "Coverage, VariantAnnotation" Homo_sapiens
TSSi "Sequencing, RNASeq, Genetics, Preprocessing" Transcription
PREDA "Software, CopyNumberVariation, GeneExpression, Genetics" "Microarray, FunctionalGenomics, Pathways, DifferentialExpression, MultipleComparison"
iontree "Metabolomics, MassSpectrometry"
rqubic "Microarray, Clustering" GeneExpression
mzR "Infrastructure, DataImport, Proteomics, Metabolomics, MassSpectrometry"
GeneExpressionSignature GeneExpression Microarray
graphite "Pathways, ThirdPartyClient, GraphAndNetwork" Network
weaver Infrastructure
PANR "NetworkInference, Visualization, GraphAndNetwork, Clustering, CellBasedAssays" Microarray
RTopper Microarray GeneSetEnrichment
DTA "Microarray, DifferentialExpression, GeneExpression, Transcription" RNASeq
EDASeq "Sequencing, RNASeq, Preprocessing, QualityControl, DifferentialExpression" "Normalization, DataImport"
dks "MultipleComparison, QualityControl" DNASeq
DiffBind "Sequencing, ChIPSeq" "Microarray, Genetics, Coverage, Normalization, Preprocessing, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse, DataImport"
AGDEX "Microarray, Genetics, GeneExpression" "DifferentialExpression, MultipleComparison"
biovizBase "Infrastructure, Visualization, Preprocessing"
CNAnorm "CopyNumberVariation, Sequencing, Cancer, Lung" "Coverage, Normalization" "Cancer, Lung"
cummeRbund "HighThroughputSequencing, HighThroughputSequencingData, RNAseq, RNAseqData, GeneExpression, DifferentialExpression, Infrastructure, DataImport, DataRepresentation, Visualization, Bioinformatics, Clustering, MultipleComparisons, QualityControl" "Sequencing, Microarray" "HighThroughputSequencing, HighThroughputSequencingData, RNAseq, RNAseqData, Bioinformatics, MultipleComparisons"
DECIPHER "Clustering, Genetics, Sequencing, Infrastructure, DataImport, Visualization, Microarray, QualityControl" SequenceMatching
GWASTools "SNP, GeneticVariability, QualityControl, Microarray" GenomeAnnotation
minfi "DNAMethylation, Microarray, TwoChannel, DataImport, Preprocessing, QualityControl" "Sequencing, WholeGenome, MethylationArray, Regression"
predictionet "GraphAndNetwork, NetworkInference" "Network, Bayesian"
stepwiseCM "Classification, Microarray, Integration" "GeneExpression, GenePrediction, DimensionReduction, Regression, SupportVectorMachine" Integration
sva "Microarray, StatisticalMethod, Preprocessing, MultipleComparison" "GeneExpression, DifferentialExpression, GenomicVariation, BatchEffect, Bayesian"
r3Cseq "Preprocessing, Sequencing" "Coverage, Normalization, MultipleComparison, DataImport"
ggbio "Infrastructure, Visualization"
MmPalateMiRNA "Microarray, TwoChannel, QualityControl, Preprocessing, DifferentialExpression, MultipleComparison, Clustering, GO, Pathways, ReportWriting, SequenceMatching" "OneChannel, TimeCourse"
isobar "Proteomics, MassSpectrometry, Bioinformatics, MultipleComparisons, QualityControl" "Bioinformatics, MultipleComparisons"
exomeCopy "CopyNumberVariation, Sequencing, Genetics" "Coverage, VariantAnnotation, VariantDetection, HiddenMarkovModel, DataImport"
ReQON "Sequencing, Preprocessing, QualityControl" "Coverage, DataImport"
CellNOptR "CellBasedAssays, CellBiology, Proteomics, Bioinformatics, TimeCourse" "Pathways, Network, GraphAndNetwork" Bioinformatics
tweeDEseq "StatisticalMethod, DifferentialExpression, Sequencing, RNASeq" "DNASeq, RIPSeq"
ncdfFlow FlowCytometry
cn.mops "Sequencing, CopyNumberVariation, Homo_sapiens, CellBiology, HapMap, Genetics" "Coverage, Bayesian" "Homo_sapiens, HapMap"
fastseg "Classification, CopyNumberVariation" "Sequencing, Genetics, Coverage, GenomeAssembly, GenomeAnnotation, Bayesian"
trigger "GeneExpression, SNP, GeneticVariability, Microarray, Genetics" GenomicVariation
spade "FlowCytometry, GraphAndNetwork, GUI, Visualization, Clustering"
sigaR "Microarray, DifferentialExpression, aCGH, GeneExpression, Pathways" "mRNAMicroarray, CopyNumberVariation"
virtualArray "Microarray, OneChannel, DataImport, Preprocessing, MultipleComparison"
ASEB Proteomics "GeneExpression, BiomedicalInformatics, GeneSetEnrichment"
AffyRNADegradation "GeneExpression, Microarray, OneChannel, Preprocessing, QualityControl"
maskBAD Microarray "Preprocessing, OneChannel"
GEWIST "MultipleComparison, Genetics"
easyRNASeq "GeneExpression, RNASeq, Genetics, Preprocessing" "Coverage, Normalization"
rhdf5 "Infrastructure, DataImport"
pcaGoPromoter "GeneExpression, Microarray, GO, Visualization" "Transcription, ChipOnChip"
manta "DifferentialExpression, RNASeq, Genetics, GeneExpression, Sequencing, QualityControl, DataImport, Visualization" ChIPSeq
BAGS Bayesian
DART "GeneExpression, DifferentialExpression, GraphAndNetwork, Pathways" "NetworkInference, Network, Classification"
phyloseq "Clustering, Classification, MultipleComparisons, QualityControl, GeneticVariability, HighThroughputSequencing" Microbiome "MultipleComparisons, HighThroughputSequencing"
deepSNV "GeneticVariability, SNP, Sequencing, Genetics, DataImport" "GenomicVariation, VariantDetection, Alignment, QualityControl"
Gviz "Visualization, Microarray" "Sequencing, Genetics, Coverage, GenomeAnnotation"
ternarynet "Software, CellBiology, GraphAndNetwork" "Genetics, Network, Bayesian"
gwascat Genetics
NarrowPeaks "Visualization, ChIPSeq, Transcription, Genetics, Sequencing, Sequencing" GenomicVariation
QUALIFIER "Infrastructure, FlowCytometry, CellBasedAssays" "Preprocessing, QualityControl, DataImport"
PING "Clustering, StatisticalMethod, Visualization, Sequencing" "Genetics, Coverage, GenomeAnnotation, NucleosomePositioning, ChIPSeq"
BRAIN "MassSpectrometry, Proteomics" "Sequencing, Genetics, SequenceMatching, DataImport"
IdMappingAnalysis "Annotation, MultipleComparison"
ffpe "Microarray, GeneExpression, QualityControl" "mRNAMicroarray, DifferentialExpression, MultipleComparison, Preprocessing"
coGPS "Microarray, DifferentialExpression" GeneSetEnrichment
HybridMTest "GeneExpression, Genetics, Microarray" "Pharmacogenomics, MultipleComparison"
BrainStars "Microarray, OneChannel, DataImport" GeneExpression
birta "Microarray, Sequencing, GeneExpression, Transcription, GraphAndNetwork" "NetworkInference, Preprocessing, Network, Bayesian, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse"
ReactomePA "Pathways, Visualization, Annotation" GeneSetEnrichment
cellGrowth "CellBasedAssays, MicrotitrePlateAssay, DataImport, Visualization, TimeCourse"
gprege "Microarray, Preprocessing, DifferentialExpression, TimeCourse" GeneExpression
VegaMC "aCGH, CopyNumberVariation" Microarray
RchyOptimyx FlowCytometry
inSilicoMerging Microarray "GeneExpression, DataImport"
BitSeq "GeneExpression, DifferentialExpression, Sequencing, RNASeq" "Coverage, Bayesian, DataImport"
CancerMutationAnalysis "Genetics, Software" "Sequencing, DriverMutation, SomaticMutation, MultipleComparison"
iBBiG "Clustering, Annotation, GeneSetEnrichment" GeneExpression
cnvGSA MultipleComparison
HiTC "Sequencing, HighThroughputSequencing" "Genetics, Coverage" HighThroughputSequencing
EBcoexpress Bayesian "GeneExpression, DifferentialExpression, Clustering"
iASeq "SNP, RNASeq, ChIPSeq" "Sequencing, ChipOnChip"
MinimumDistance "Microarray, SNP, CopyNumberVariation" GenotypingArray
motifRG "Transcription, MotifDiscovery" "Sequencing, Genetics, MotifAnnotation, Regression, SequenceMatching, DataImport"
categoryCompare "Annotation, GO, MultipleComparison, Pathways, GeneExpression"
DirichletMultinomial "Sequencing, Clustering, Classification" Microbiome
ddgraph GraphAndNetwork "Transcription, GeneRegulation, GeneTarget"
cancerclass "Cancer, Microarray, Classification, Visualization" Cancer
staRank "MultipleComparison, CellBiology, CellBasedAssays, MicrotitrePlateAssay"
MiRaGE "Microarray, GeneExpression, RNASeq, RNAseqData, Sequencing, Sequencing, SAGE" "GeneRegulation, GeneTarget" RNAseqData
rols "Software, Annotation, MassSpectrometry, GO"
flowQB FlowCytometry "QualityControl, Regression"
annmap "Annotation, Microarray, OneChannel, ReportWriting, Transcription, Visualization" "ExonArray, Sequencing, Genetics, Coverage, GenomeAnnotation"
flowPeaks "FlowCytometry, Clustering, Gating" Gating
FunciSNP "Infrastructure, DataRepresentation, DataImport, SequenceMatching, Annotation"
DSS "Sequencing, RNASeq, ChIPSeq, DNAMethylation, DifferentialExpression" Bayesian
PWMEnrich "SequenceMatching, GenomicSequence, Software" "Sequencing, Genetics, DataImport" GenomicSequence
OSAT "DataRepresentation, Visualization, ExperimentalDesign, QualityControl" Microarray
KEGGprofile Pathways
synapter "MassSpectrometry, Proteomics, GUI" QualityControl
bsseq DNAMethylation "Sequencing, WholeGenome, Genetics, Coverage, GenomeAnnotation"
DBChIP "ChIPSeq, Sequencing, Transcription, Genetics" "RNASeq, DifferentialExpression"
gmapR Alignment "Genetics, GenomeAnnotation, VariantAnnotation"
CorMut Sequencing
iPAC "Clustering, Proteomics" "Sequencing, Microarray, mRNAMicroarray, Genetics, SomaticMutation, DimensionReduction, DifferentialExpression, SequenceMatching, MultipleComparison, DataImport"
networkBMA "GraphsAndNetworks, NetworkInference" "GeneExpression, GeneTarget, Network, Bayesian" GraphsAndNetworks
waveTiling "Microarray, DifferentialExpression, TimeCourse, GeneExpression" "Sequencing, Genetics, Preprocessing, ExonArray, OneChannel, TwoChannel, SequenceMatching, DataImport"
triform "Sequencing, ChIPSeq" "Transcription, ChipOnChip, Coverage, Preprocessing"
PADOG "Microarray, OneChannel, TwoChannel" "GeneExpression, ChipOnChip, Preprocessing, MultipleComparison, QualityControl, TimeCourse"
RMassBank "Bioinformatics, MassSpectrometry, Metabolomics, Software" Bioinformatics
ChIPXpress "ChIPchip, ChIPSeq" "GeneExpression, Transcription, RNASeq, ChipOnChip, GeneTarget"
MotifDb "GenomicSequence, MotifAnnotation" "Sequencing, Genetics, SequenceMatching, DataImport" GenomicSequence
GeneNetworkBuilder "Sequencing, Microarray, GraphAndNetwork" "GeneExpression, Transcription, Network"
EasyqpcR "qPCR, GeneExpression" "Normalization, DataImport"
CNORfuzzy Network "CellBiology, Proteomics, SystemsBiology, Pathways, CellBasedAssays, TimeCourse"
methyAnalysis "Microarray, DNAMethylation, Visualization" "Sequencing, MethylationArray, Genetics, Coverage, DifferentialMethylation"
fmcsR "MicrotitrePlateAssay, CellBasedAssays, Visualization, Infrastructure, DataImport, Clustering, Proteomics"
lmdme "Microarray, OneChannel, TwoChannel, Visualization, DifferentialExpression, ExperimentData, Cancer" "ExperimentData, Cancer"
hapFabia "Genetics, GeneticVariability, SNP, Sequencing, Sequencing, Visualization, Clustering, SequenceMatching, Homo_sapiens, Software" "CopyNumberVariation, Microarray, mRNAMicroarray, MultipleComparison" Homo_sapiens
hpar "Proteomics, Homo_sapiens, CellBiology" Homo_sapiens
Risa "Annotation, DataImport, MassSpectrometry" "Microarray, FlowCytometry, Proteomics, Preprocessing, OneChannel"
gCMAP "Microarray, Software, Pathways, Annotation" "GeneExpression, DifferentialExpression, GeneSetEnrichment, Preprocessing, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse"
motifStack "SequenceMatching, GenomicsSequence, Visualization" "Microarray, ChIPchip, ChIPSeq, MotifAnnotation" GenomicsSequence
DeconRNASeq "ExperimentData, DifferentialExpression" "Microarray, TissueMicroarray, Bayesian" ExperimentData
ReportingTools "Software, Visualization, Microarray, RNASeq, GO, Bioinformatics, DataRepresentation, Enrichment, GeneSetEnrichment" Sequencing "Bioinformatics, Enrichment"
SCAN.UPC "Software, Microarray, Preprocessing, RNASeq, TwoChannel, OneChannel" "Sequencing, Genetics, Normalization, ExonArray, GeneExpression, DifferentialExpression, SequenceMatching, MultipleComparison, DataImport"
agilp StatisticalMethod "GeneExpression, Microarray, Regression"
CNORdt "CellBasedAssays, CellBiology, Proteomics, TimeCourse"
bigmemoryExtras "Infrastructure, DataRepresentation"
CNORode "CellBasedAssays, CellBiology, Proteomics, Bioinformatics, TimeCourse" Bioinformatics
HMMcopy "Sequencing, Preprocessing, Visualization, CopyNumberVariation, Microarray" "WholeGenome, Coverage"
HTSeqGenie NA
Rcade "DifferentialExpression, GeneExpression, Transcription, ChIPSeq, Sequencing, Genetics" "Coverage, Bayesian, DataImport"
TransView "DNAMethylation, GeneExpression, Transcription, Microarray, Sequencing, Sequencing, ChIPSeq, RNASeq, MethylSeq, DataImport, Visualization, Clustering, MultipleComparison" "Genetics, Coverage"
NOISeq "RNASeq, DifferentialExpression, Visualization, Sequencing" WholeGenome
chroGPS "Visualization, Clustering"
VariantTools "Genetics, GeneticVariability, Sequencing" "WholeGenome, Coverage, GenomeAnnotation, VariantAnnotation, QualityControl"
rSFFreader "DataImport, Sequencing" "Genetics, Coverage, SequenceMatching"
matchBox "Software, Annotation, Microarray, MultipleComparison, Visualization" "GeneExpression, mRNAMicroarray, Pathways"
RIPSeeker "Sequencing, RIPSeq" "Genetics, Coverage, Alignment, DataImport"
illuminaio "Infrastructure, DataImport" Microarray
SNAGEE "Microarray, OneChannel, TwoChannel, QualityControl" GeneExpression
UniProt.ws "Annotation, Infrastructure"
plrs Regression "GeneExpression, Bayesian"
pvca "Microarray, BatchEffect" GeneExpression
pRoloc "Proteomics, MassSpectrometry, Classification, Clustering" QualityControl
DriverNet Network "CopyNumberVariation, GeneExpression"
bumphunter "DNAMethylation, Epigenetics, Infrastructure, MultipleComparison" "Transcription, Sequencing, Genetics, Coverage, GeneTarget"
wateRmelon "DNAMethylation, Microarray, TwoChannel, Preprocessing, QualityControl" "MethylationArray, mRNAMicroarray, Normalization, CpGIsland, OneChannel, DifferentialExpression, MultipleComparison, TimeCourse"
ensemblVEP Annotation "Sequencing, Genetics, Coverage, GenomeAnnotation, VariantAnnotation, DataImport"
GraphPAC "Clustering, Proteomics"
iBMQ "Microarray, Preprocessing, GeneExpression, SNP" "DifferentialExpression, Bayesian"
RSVSim Sequencing "WholeGenome, Genetics, Coverage, GenomeAnnotation, VariantAnnotation, VariantDetection, SequenceMatching, DataImport"
rTANDEM "MassSpectrometry, Proteomics"
Rbowtie "Sequencing, Alignment"
QuasR "Genetics, Preprocessing, Sequencing, ChIPSeq, RNASeq, MethylSeq" "Coverage, GenomeAnnotation, Alignment, QualityControl"
casper "GeneExpression, DifferentialExpression, Transcription, RNASeq, Sequencing" "DenovoGenome, Genetics, AlternativeSplicing, Coverage, GenomeAnnotation, VariantAnnotation"
clipper NA
PathNet "Pathways, DifferentialExpression, MultipleComparison" "GeneExpression, Microarray, mRNAMicroarray, GeneSetEnrichment, NetworkEnrichment, Network"
DrugVsDisease "Microarray, GeneExpression, Clustering" "DifferentialExpression, GeneSetEnrichment, GenomeAnnotation, NetworkEnrichment, MultipleComparison, Preprocessing, Network, Classification, OneChannel, TwoChannel, QualityControl, TimeCourse, DataImport"
MethylSeekR "Sequencing, MethylSeq, DNAMethylation" Coverage
HTSFilter "Sequencing, RNASeq, Preprocessing, DifferentialExpression" "GeneExpression, ExperimentalDesign, Normalization"
rBiopaxParser DataRepresentation
SomatiCA "Sequencing, CopyNumberVariation" "Microarray, GenomeAnnotation, Bayesian"
lpNet Network "Microarray, mRNAMicroarray, GeneSignaling, NetworkInference, Pathways, DecisionTree, GraphAndNetwork"
MineICA "Visualizations, MultipleComparison" "Microarray, Pathways, Preprocessing, TwoChannel, GraphAndNetwork" Visualizations
cisPath Proteomics "GeneTarget, Network, GraphAndNetwork"
biomvRCNS "aCGH, CopyNumberVariation, Microarray, Sequencing, Sequencing, Visualization, Genetics" "Coverage, HiddenMarkovModel"
CAGEr "Preprocessing, Sequencing, HighThroughputSequencing, Transcription, Clustering, Visualization" "GeneExpression, Genetics, Normalization, SequenceMatching" HighThroughputSequencing
chimera Infrastructure "Sequencing, Genetics, Coverage, Alignment, DataImport"
DESeq2 "Sequencing, ChIPSeq, RNASeq, SAGE, DifferentialExpression" GeneExpression
proteinProfiles "Annotation, Proteomics, TimeCourse, Clustering"
SANTA "Network, NetworkEnrichment, Clustering" GraphAndNetwork
gCMAPWeb "GUI, GeneSetEnrichment, Visualization" "GeneExpression, Transcription, Microarray, DifferentialExpression, GeneSignaling, Pathways"
ARRmNormalization "DNAMethylation, TwoChannel, Preprocessing, Microarray" "Normalization, Regression"
deltaGseg "Proteomics, TimeCourse, Visualization, Clustering"
dexus "Sequencing, Mus_musculus, Homo_sapiens, Zea_Mays, Macaca_mulatta, Pan_troglodytes, RNASeq, GeneExpression, DifferentialExpression, CellBiology, HapMap, RNAseqData, Classification, QualityControl" Bayesian "Mus_musculus, Homo_sapiens, Zea_Mays, Macaca_mulatta, Pan_troglodytes, HapMap, RNAseqData"
epigenomix "ChIPSeq, GeneExpression, DifferentialExpression, Classification" "Transcription, Sequencing, Microarray, Genetics, Coverage, HistoneModification, Normalization, Preprocessing, Bayesian"
HCsnip "Microarray, aCGH, GeneExpression, Clustering" "Pathways, DifferentialExpression"
jmosaics "ChIPSeq, Sequencing, Transcription, Genetics"
pathview "Pathways, GraphsAndNetworks, NetworkVisualization, GeneSetEnrichment, DifferentialExpression, GeneExpression, Microarray, RNAseq, Genetics, Metabolomics, Proteomics, Bioinformatics" "GeneTarget, GraphAndNetwork" "GraphsAndNetworks, NetworkVisualization, RNAseq, Bioinformatics"
RNASeqPower RNASeq "GeneExpression, Sequencing, Coverage, GeneTarget"
SeqArray "Infrastructure, Sequencing, Genetics" VariantAnnotation
SPEM "Network, NetworkInference, Software" GeneExpression
BaseSpaceR "Infrastructure, DataRepresentation, ConnectTools, Software, DataImport, HighThroughputSequencing, Sequencing, Genetics" "ConnectTools, HighThroughputSequencing"
CNORfeeder "CellBasedAssays, CellBiology, Proteomics, NetworkInference" "Network, Bayesian, GraphAndNetwork, TimeCourse"
eiR "Infrastructure, DataImport, Clustering, Proteomics" "CellBasedAssays, MicrotitrePlateAssay"
ROntoTools "Network, Microarray, GraphAndNetwork" "Pathways, ThirdPartyClient"
AnnotationHub "Annotation, Infrastructure"
metagenomeSeq "DifferentialExpression, Metagenomics, Visualization" "Sequencing, Microarray, Normalization, Preprocessing, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse"
DASiR Annotation "Sequencing, Genetics, Coverage, GenomeAnnotation, Network, SequenceMatching, DataImport"
SeqGSEA "Sequencing, RNASeq, GeneSetEnrichment, GeneExpression, DifferentialExpression" "DifferentialSplicing, ChIPSeq"
geNetClassifier "Classification, DifferentialExpression, Microarray" "GeneExpression, Network, Clustering, NetworkInference, GraphAndNetwork"
copynumber "aCGH, SNP, CopyNumberVariation, Genetics, Visualization" Regression
antiProfiles "GeneExpression, Classification"
PAPi "MassSpectrometry, Metabolomics" "Pathways, ThirdPartyClient"
GENE.E ThirdPartyClient
MMDiff "ChIPSeq, MultipleComparison" "Sequencing, Genetics, Coverage, HistoneModification, Normalization, DataImport"
piano "Microarray, Preprocessing, QualityControl, DifferentialExpression, Visualization, GeneExpression, GeneSetEnrichment, Pathways"
prebs "Microarray, RNASeq, Sequencing, GeneExpression, Preprocessing" "WholeGenome, Genetics, OneChannel, DataImport"
triplex "SequenceMatching, GeneRegulation"
BiSeq "Genetics, Sequencing, MethylSeq, DNAMethylation" Coverage
SplicingGraphs "Genetics, Annotation, DataRepresentation, Visualization, Sequencing, RNASeq, GeneExpression" "Coverage, Alignment, DataImport"
sSeq RNASeq GeneExpression
XVector "Infrastructure, DataRepresentation"
clonotypeR Sequencing Alignment
flowFit "FlowCytometry, CellBasedAssays"
plethy "DataImport, biocViews, Infastructure, DataRepresentation, TimeCourse" "biocViews, Infastructure"
EBSeq "StatisticalMethod, DifferentialExpression, MultipleComparison, RNASeq, Sequencing" "GeneExpression, DNASeq"
prot2D "DifferentialExpression, MultipleComparison, Proteomics" "Microarray, Normalization, Preprocessing, GeneExpression, OneChannel, TwoChannel, QualityControl, TimeCourse"
tRanslatome "CellBiology, GeneRegulation, GeneExpression, DifferentialExpression, Microarray, Sequencing, QualityControl, GO, MultipleComparison" "Pathways, Preprocessing, Network, Clustering, RNASeq, ChIPSeq, OneChannel, TwoChannel, TimeCourse"
vtpnet Network "Transcription, Sequencing, Genetics, Coverage, GenomeAnnotation, MotifAnnotation, VariantAnnotation, GraphAndNetwork"
flowBeads "Infrastructure, FlowCytometry, CellBasedAssays"
spliceR "DifferentialExpression, Sequencing, RNASeq, RNAseqData, software, Visualization" "AlternativeSplicing, Classification, Clustering, GeneExpression, QualityControl, DataImport" "RNAseqData, software"
cleaver Proteomics "Sequencing, Genetics, SequenceMatching, DataImport"
customProDB Proteomics
mitoODE "ExperimentData, TimeCourse, CellBasedAssays, Preprocessing" ExperimentData
NetSAM "Visualization, Network" GraphAndNetwork
paircompviz GraphAndNetwork MultipleComparison
pathifier Network "GeneExpression, GeneRegulation, Pathways"
RDAVIDWebService "Visualization, DifferentialExpression, ExperimentData, Cancer" "MultipleComparison, GraphAndNetwork" "ExperimentData, Cancer"
rTRM "Transcription, Network, GeneRegulation, GraphAndNetwork"
maPredictDSC "Microarray, Classification" "Preprocessing, OneChannel, TwoChannel, DifferentialExpression, MultipleComparison, QualityControl, TimeCourse"
cleanUpdTSeq "Sequencing, SequenceMatching, Genetics, GeneRegulation" "Coverage, GenomeAnnotation, Classification"
OmicCircos "Visualization, StatisticalMethod, Annotation" "Sequencing, Genetics, Coverage, GenomeAnnotation"
seqCNA "CopyNumberVariation, Genetics, Sequencing" "Microarray, GenomicVariation, GenomeAnnotation, StructuralVariation, Normalization"
SigFuge "Clustering, Visualization, RNASeq" "Sequencing, Genetics, Coverage, GenomeAnnotation, Network"
TargetScore miRNA Bayesian
CSSP "ChIPseqData, Sequencing, QualityControl" Bayesian ChIPseqData
cobindR "ChIPSeq, CellBiology, MultipleComparison, SequenceMatching" Transcription
intansv "Genetics, Annotation, Sequencing, Software" "WholeGenome, Coverage, GenomicVariation, GenomeAnnotation, StructuralVariation"
msmsEDA "Software, MassSpectrometry, Proteomics" "BatchEffect, QualityControl"
RRHO "Genetics, SequenceMatching, Microarray, Transcription"
msmsTests "Software, MassSpectrometry, Proteomics" "GeneExpression, DifferentialExpression, BatchEffect, QualityControl"
Rchemcpp "Bioinformatics, CellBasedAssays, Clustering, DataImport, Infrastructure, MicrotitrePlateAssay, Proteomics, Software, Visualization" Bioinformatics
rfPred "Software, Homo-sapiens, Annotation, Classification" "Sequencing, Genetics, Coverage, FunctionalPrediction, DataImport" Homo-sapiens
RTN "NetworkInference, NetworkAnalysis, NetworkEnrichment, GeneRegulation, GeneExpression, GraphsAndNetworks" "Transcription, GeneSetEnrichment, Network" "NetworkAnalysis, GraphsAndNetworks"
SeqVarTools "SNP, GeneticVariability, Sequencing, Genetics"
SpacePAC "Clustering, Proteomics"
trio "SNP, GeneticVariability, Microarray, Genetics" LinkageDisequilibrium
SwimR Visualization
supraHex "Bioinformatics, Clustering, Visualization, GeneExpression" Bioinformatics
ASSET Software
ChemmineOB Cheminformatics
qusage "GeneSetEnrichment, Microarray, RNASeq, Software" "GeneExpression, DifferentialExpression, Pathways, Preprocessing, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse"
TCC "Sequencing, DifferentialExpression, RNASeq" "GeneExpression, OneChannel, TwoChannel, Genetics, Normalization, ChIPSeq"
BiGGR "Network, Visualization, Metabolomics" "Pathways, GraphAndNetwork"
chipenrich "Software, GeneSetEnrichment" "Transcription, Sequencing, RNASeq, ChipOnChip, Pathways, QualityControl"
Roleswitch miRNA "Transcription, GenomeAnnotation, SequenceMatching"
BADER "Sequencing, RNASeq, DifferentialExpression, Software, SAGE" "GeneExpression, Bayesian"
mzID "DataImport, MassSpectrometry, Proteomics"
ArrayTV CopyNumberVariation "Sequencing, Microarray, GenotypingArray"
BiRewire Network "Sequencing, GraphAndNetwork"
GOSim "GO, Clustering, Software, Network, DecisionTree" "Normalization, Pathways"
neaGUI "Microarray, DifferentialExpression, GUI" "GeneSetEnrichment, NetworkEnrichment, Pathways, Network"
omicade4 "Software, Clustering, Classification, MultipleComparison" Microarray
ProCoNA "GraphAndNetwork, Software, Proteomics" "Network, MassSpectrometry, QualityControl"
rTRMui "Transcription, Network, GeneRegulation, GraphAndNetwork, GUI"
SimBindProfiles "Microarray, Software"
STRINGdb Network "Microarray, RNASeq"
AllelicImbalance "Genetics, Infrastructure, Allelic Imbalance, AI, ASE, Sequencing" "GeneExpression, DataImport" "Allelic Imbalance, AI, ASE"
ampliQueso "ReportWriting, Transcription, GeneExpression, DifferentialExpression, Sequencing, RNASeq, Visualization" "Microarray, Coverage"
bioassayR "MicrotitrePlateAssay, CellBasedAssays, Visualization, Infrastructure, DataImport, Proteomics"
CexoR "Transcription, Genetics, Sequencing"
dagLogo "SequenceMatching, GenomicsSequence, Visualization" "WholeGenome, GenomeAnnotation" GenomicsSequence
DNaseR "Transcription, Genetics" Preprocessing
epivizr "Visualization, Infrastructure, GUI" "Sequencing, Genetics, Coverage, GenomeAnnotation"
exomePeak "Sequencing, MethylSeq, RNASeq" "Genetics, Coverage, DifferentialMethylation, MultipleComparison, DataImport"
flowMap "MultipleComparison, FlowCytometry"
methylMnM "Software, DNAMethylation, Sequencing" "Normalization, RNASeq, ChIPSeq, DifferentialExpression"
MSstats "MassSpectrometry, Proteomics, Software" "Normalization, QualityControl, TimeCourse"
openCyto "FlowCytometry, DataImport, Preprocessing, DataRepresentation"
qcmetrics "Software, QualityControl, Proteomics, Microarray, MassSpectrometry, Visualization"
shinyTANDEM "MassSpectrometry, Proteomics"
spliceSites "RNASeq, GeneExpression, DifferentialExpression, Proteomics" SequenceMatching
sRAP "GeneExpression, RNASeq, Microarray, Preprocessing, QualityControl, StatisticalMethod, DifferentialExpression, Visualization, GeneSetEnrichment, GO" "Normalization, Pathways"
TFBSTools "MotifAnnotation, GeneRegulation, MotifDiscovery" "Transcription, Alignment"
FGNet "Annotation, GO, Pathways, GeneSetEnrichment, Networks, NetworkVisualization" "FunctionalGenomics, NetworkEnrichment, Network, Clustering" "Networks, NetworkVisualization"
flipflop RNASeq "GeneExpression, Coverage, GenePrediction, Alignment"
ChAMP "Bioinformatics, DNAMethylation, DataImport, IlluminaChip, Preprocessing, QualityControl, Software, DifferentialMethylation, SNP, CopyNumberVariants" "Microarray, MethylationArray, Normalization, TwoChannel" "Bioinformatics, IlluminaChip, CopyNumberVariants"
interactiveDisplay "GO, GeneExpression, Microarray, Sequencing, Classification, Network, QualityControl, Visualization, Visualization, Genetics, DataRepresentation, GUI, AnnotationData" AnnotationData
metaSeq "RNASeq, DifferentialExpression, Sequencing"
h5vc NA
PSICQUIC "DataImport, GraphAndNetwork, ThirdPartyClient" Proteomics
CNVrd2 "High Throughput Sequencing, CNV, SNP." "Sequencing, Microarray, Coverage, LinkageDisequilibrium, Clustering, CopyNumberVariation, DataImport" "High Throughput Sequencing, CNV, SNP."
GOTHiC "Sequencing, Preprocessing, Epigenetics" "Genetics, Coverage, GenomeAnnotation, SequenceMatching, DataImport"
CRISPRseek "GeneRegulation, SequenceMatching" "Sequencing, Genetics, GenomeAnnotation, Alignment, DataImport"
mmnet "Bioinformatics, GraphsAndNetworks, HighThroughputSequencing, Pathways" "Microbiome, SystemsBiology, Network, GraphAndNetwork" "Bioinformatics, GraphsAndNetworks, HighThroughputSequencing"
PECA "Software, Preprocessing, Microarray, DifferentialExpression, GeneExpression" "ExonArray, Proteomics, DifferentialSplicing, Normalization, QualityControl"
flowMatch "Clustering, FlowCytometry" CellBasedAssays
ccrepe "Statistics, Metagenomics, Bioinformatics, Software" "Statistics, Bioinformatics"
PhenStat NA
roar "Sequencing, RNASeq, Transcription"
flowBin "CellBasedAssays, FlowCytometry" Clustering
geneRxCluster "Sequencing, Clustering, Genetics" "Coverage, GeneTarget, MultipleComparison"
asmn "DNAMethylation, TwoChannel, Preprocessing, QualityControl" "OneChannel, Normalization"
COHCAP "DNAMethylation, Microarray, MethylSeq, Epigenetics" "GeneExpression, MethylationArray, DifferentialExpression, DifferentialMethylation, QualityControl"
GeneOverlap "MultipleComparison, Visualization" "RNASeq, ChIPSeq"
AtlasRDF "Microarray, DataImport, GeneSetEnrichment, GeneExpression, DifferentialExpression, DataRepresentation" "Sequencing, mRNAMicroarray, FunctionalGenomics, Pathways"
BEAT "Genetics, MethylSeq, Software, DNAMethylation, Epigenetics"
iClusterPlus "Genomic data, Microarray" Clustering Genomic data
biosvd "TimeCourse, Visualization" GeneRegulation
ELBOW "Technology, Microarray, RNASeq, Sequencing, Sequencing, Software, MultiChannel, OneChannel, TwoChannel, GeneExpression"
savR Sequencing
trackViewer "GenomicsSequence, Visualization" "Sequencing, Genetics, Coverage" GenomicsSequence
SomaticSignatures "Sequencing, SomaticMutation, Visualization, Clustering, HighThroughputSequencingData, Cancer, PrinicpalComponent, GenomicVariation, StatisticalMethod" "HighThroughputSequencingData, Cancer"
Mirsynergy Clustering
MIMOSA "FlowCytometry, CellBasedAssays"
CNEr "GeneRegulation, Visualization, DataImport" GenomeAnnotation
COMPASS FlowCytometry Bayesian
GSCA "GeneExpression, Visualization, GUI" "ChipOnChip, GeneSignaling, PeakDetection, Pathways, Network"
CopyNumber450k "DNAMethylation, Microarray, Preprocessing, QualityControl, CopyNumberVariation" "MethylationArray, mRNAMicroarray, Normalization, TwoChannel"
sangerseqR "Sequencing, SNP, Visualization" "Genetics, SangerSeq, SequenceMatching, DataImport"
unifiedWMWqPCR "DifferentialExpression, GeneExpression, MicrotitrePlateAssay, MultipleComparison, QualityControl, Software, Visualization, qPCR"
DMRcate "DifferentialMethylation, IlluminaChip, Preprocessing, SNP" "GeneExpression, Microarray, MethylationArray, Genetics, DifferentialExpression, GenomeAnnotation, DNAMethylation, OneChannel, TwoChannel, MultipleComparison, QualityControl, TimeCourse" IlluminaChip
EDDA "Bioinformatics, DifferentialExpression" "Sequencing, ExperimentalDesign, Normalization, RNASeq, ChIPSeq" Bioinformatics
scsR Preprocessing "Sequencing, Genetics, Network, SequenceMatching, DataImport"
Clomial "Genetics, GeneticVariability, Sequencing, Clustering, MultipleComparison, Bayesian, DNASeq, ExomeSeq, TargetedResequencing"
dualKS "Microarray, Classification" "GeneExpression, Preprocessing, OneChannel"
alsace "Metabolomics, Preprocessing" Clustering
Basic4Cseq "Visualization, QualityControl" "Sequencing, Genetics, Coverage, Alignment, SequenceMatching, DataImport"
CAFE "GeneExpression, Microarray, OneChannel, GeneSetEnrichment" "Sequencing, Genetics, Coverage, Preprocessing"
COPDSexualDimorphism "Software, AssayDomain, Microarray, GeneExpression, DNAMethylation, DifferentialExpression" "Sequencing, Genetics, Coverage, Regression"
INPower SNP "Genetics, Regression"
massiR "Software, Microarray, GeneExpression, Clustering, Classification, QualityControl"
metaseqR "Software, GeneExpression, DifferentialExpression, WorkflowStep, Preprocessing, QualityControl, Normalization, ReportWriting, RNASeq"
MLSeq "Bioinformatics, Classification, Clustering" "Sequencing, Microarray, Preprocessing, RNASeq, ChIPSeq, OneChannel, TwoChannel, DifferentialExpression, MultipleComparison, QualityControl, TimeCourse" Bioinformatics
rpx "Proteomics, MassSpectrometry, DataImport, ThirdPartyClient"
QDNAseq "CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation, Preprocessing, QualityControl, Sequencing"
Rcpi "Software, DataImport, DataRepresentation, FeatureExtraction, Cheminformatics, BiomedicalInformatics, Proteomics, GO, GraphAndNetwork, SystemsBiology"
sapFinder "MassSpectrometry, Proteomics, SNP, RNASeq, Visualization, ReportWriting" "GenomeAnnotation, VariantAnnotation, VariantDetection"
UNDO Software Preprocessing
viper "SystemsBiology, NetworkEnrichment, GeneExpression, FunctionalPrediction, GeneRegulation" "GeneTarget, NetworkInference, Network"
messina "GeneExpression, DifferentialExpression, BiomedicalInformatics, Classification, Survival"
nondetects "Software, AssayDomain, GeneExpression, Technology, qPCR, WorkflowStep, Preprocessing"
ASSIGN "Software, GeneExpression, Pathways, Bayesian"
ABSSeq DifferentialExpression
ChIPQC "Sequencing, ChIPSeq, QualityControl, ReportWriting" "ChipOnChip, Genetics, Coverage"
CompGO "GeneSetEnrichment, MultipleComparison, GO, Visualization" "Transcription, GenomeAnnotation, DataImport"
flowCyBar "CellBasedAssays, Clustering, FlowCytometry, Software, Visualization"
FRGEpistasis "Genetics, NetworkInference, GeneticVariability, Software" "GenomicVariation, Regression"
Rariant "Sequencing, StatisticalMethod, GenomicVariation, SomaticMutation, VariantDetection, Visualization"
flowCL FlowCytometry GraphAndNetwork
metaMS "MassSpectrometry, Metabolomics"
CoverageView "Visualization, RNASeq, ChIPSeq, Sequencing, Technology, Software" "Coverage, NucleosomePositioning, Normalization, DataImport"
VariantFiltering "Genetics, Homo_sapiens, Annotation, SNP, Sequencing, HighThroughputSequencing" "Homo_sapiens, HighThroughputSequencing"
DMRforPairs "Microarray, DNAMethylation, DifferentialMethylation, ReportWriting, Visualization, Annotation" "MethylationArray, MultipleComparison"
Sushi "DataRepresentation, Visualization, Genetics, Sequencing, Infrastructure"
npGSEA "GeneSetEnrichment, Microarray, StatisticalMethod, Pathways"
TitanCNA "Sequencing, WholeGenome, DNASeq, ExomeSeq, StatisticalMethod, CopyNumberVariation, HiddenMarkovModel, Genetics, GenomicVariation" "Microarray, mRNAMicroarray, Preprocessing, Clustering"
compcodeR "RNASeq, DifferentialExpression" "Normalization, Bayesian"
RefNet GraphAndNetwork "ThirdPartyClient, DataImport"
gaucho "Software, Genetics, SNP, Sequencing, SomaticMutation" GraphAndNetwork
MeSHDbi "Annotation, AnnotationData, Infrastructure" AnnotationData
meshr "AnnotationData, FunctionalAnnotation, Bioinformatics, Statistics, Annotation, MultipleComparisons" "Pathways, Clustering, GeneExpression, RNASeq, GeneSetEnrichment, QualityControl, DataImport" "AnnotationData, FunctionalAnnotation, Bioinformatics, Statistics, MultipleComparisons"
NetPathMiner "GraphAndNetwork, Pathways, Network, Clustering, Classification" "GeneExpression, Microarray, Coverage"
ChIPseeker "Annotation, ChIPSeq, Software, Visualization, MultipleComparison" "Coverage, GeneRegulation"
fastLiquidAssociation "Software, Bioinformatics" "Genetics, Pathways, GeneExpression, CellBiology, TimeCourse" Bioinformatics
hiAnnotator "Software, Annotation"
blima "Microarray, Preprocessing, Normalization" DifferentialExpression
monocle "Sequencing, RNASeq, GeneExpression, DifferentialExpression, Infrastructure, DataImport, DataRepresentation, Visualization, Clustering, MultipleComparison, QualityControl"
HDTD "GeneExpression, DifferentialExpression, Genetics, Microarray, RNASeq, StatisticalMethod, Software"
MoPS "GeneRegulation, Classification, TimeCourse, Regression"
DupChecker Preprocessing "GeneExpression, GeneTarget"
MethylAid "DNAMethylation, Microarray, TwoChannel, QualityControl, Visualization, GUI" "MethylationArray, BatchEffect"
msQC "Proteomics, MassSpectrometry, QualityControl, Visualization, ReportWriting"
flowClean "FlowCytometry, QualityControl" CellBasedAssays
cosmiq "MassSpectrometry, Metabolomics" "PeakDetection, Preprocessing"
wavClusteR "Sequencing, Software" "Genetics, Coverage, GenomeAnnotation, MotifAnnotation, DataImport"
RUVSeq "DifferentialExpression, Preprocessing, RNASeq, Software" "Sequencing, DNASeq, Normalization, ChIPSeq"
GSAR "Software, StatisticalMethod, DifferentialExpression" "Network, GraphAndNetwork"
DEGreport "DifferentialExpression, Visualization, RNASeq, ReportWriting" GeneExpression
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