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Bioconductor - Removed Packages

A list of packages removed from Bioconductor along with their last-available landing pages.

Software Packages:

• Director
• erma
• girafe
• RBioinf
• Rtreemix
• synapter
• zlibbioc
• AneuFinder
• BEARscc
• CBEA
• chromstaR
• coMET
• crossmeta
• dce
• DeProViR
• DIAlignR
• GeneGeneInteR
• genoCN
• gespeR
• GraphPAC
• HTSeqGenie
• iPAC
• MAGeCKFlute
• netDx
• NeuCA
• PanViz
• pareg
• paxtoolsr
• PICS
• PING
• QuartPAC
• ReactomeContentService4R
• RGMQL
• SpacePAC
• staRank
• STdeconvolve
• supraHex
• trigger
• TypeInfo

Experiment Data Packages:

• parathyroidSE
• benchmarkfdrData2019
• synapterdata

Annotation Data Packages:

• mirbase.db
• targetscan.Hs.eg.db
• targetscan.Mm.eg.db

Workflow Packages:

• BiocMetaWorkflow

Software Packages:

• BiocOncoTK
• psygenet2r
• rDGIdb
• RNAinteract
• ATACCoGAPS
• biodbExpasy
• biodbKegg
• brainflowprobes
• BRGenomics
• CellaRepertorium
• microbiomeMarker
• MQmetrics
• nanotatoR
• netOmics
• Pi
• polyester
• RandomWalkRestartMH
• Risa
• single
• SummarizedBenchmark

Note: zlibbioc is deprecated but will be given an extra 6 months (removed in 3.22) to allow multiple dependencies to adapt.

Experiment Data Packages:

• DmelSGI
• RNAinteractMAPK

Software Packages:

• CancerInSilico
• cellHTS2
• CNVgears
• compartmap
• ensemblVEP
• HumanTranscriptomeCompendium
• maigesPack
• MMAPPR2
• openPrimeRui
• pwOmics
• restfulSE
• beadarraySNP
• BDMMAcorrect
• BHC
• biodbLipidmaps
• BioNetStat
• CancerSubtypes
• cliqueMS
• contiBAIT
• CoRegNet
• CORREP
• crisprseekplus
• DNABarcodes
• dpeak
• EBSeqHMM
• eegc
• enrichTF
• exomePeak2
• farms
• FCBF
• flowMap
• FoldGO
• FScanR
• FunChIP
• GOSim
• ImmuneSpaceR
• InterMineR
• IntOMICS
• IRISFGM
• iterClust
• metagene
• MetaVolcanoR
• miRmine
• MobilityTransformR
• multiOmicsViz
• NeighborNet
• oneSENSE
• pathVar
• pcxn
• PERFect
• phemd
• PloGO2
• proteasy
• PSEA
• RefPlus
• ReQON
• RIPAT
• RLSeq
• SimBindProfiles
• SMAP
• sparseDOSSA
• SpidermiR
• SQUADD
• StarBioTrek
• STROMA4
• TimiRGeN
• TNBC.CMS

Experiment Data Packages:

• MMAPPR2data
• pcxnData
• restfulSEData
• RLHub

Software Packages:

• BGmix
• bigPint
• biodbMirbase
• BioMM
• Clonality
• COHCAP (maintainer requested immediate removal)
• CSSP
• deco
• DeepBlueR
• DMRforPairs
• exomeCopy
• fcoex
• gaggle
• GCSscore
• genbankr
• GISPA
• GOsummaries
• GRridge
• HPAStainR
• imageHTS
• IntOMICS (because of naming trademark issue)
• LineagePulse
• logitT
• LowMACA
• LPEadj
• macat
• mAPKL
• mbOmic
• Metab
• MSstatsSampleSize
• multiSight
• netbiov
• OmicsLonDA
• PFP
• plethy
• pwrEWAS
• qrqc
• Ringo
• SCATE
• SEPIRA
• seqbias
• seqCNA
• SISPA
• snapCGH
• sscore
• Travel
• trena

Experiment Data Packages:

• ccTutorial
• ChIC.data
• mAPKLData
• MAQCsubsetILM
• MIGSAdata
• pwrEWAS.data
• SCATEData
• seqCNA.annot
• stjudem

Software Packages:

• alpine
• ArrayExpressHTS
• ASpediaFI
• BiocDockerManager
• ChIC
• chromswitch
• copynumber
• CopywriteR
• dasper
• epihet
• GAPGOM
• GeneAccord
• genotypeeval
• maanova
• metavizr
• MethCP
• MIGSA
• MIMOSA
• NanoStringQCPro
• NBSplice
• netboxr
• NxtIRFcore
• ODER
• pkgDepTools
• PrecisionTrialDrawer
• proBatch
• proFIA
• pulsedSilac
• savR
• sigPathway
• STAN
• TarSeqQC
• tscR

Experiment Data Packages:

• alpineData
• plasFIA

Software Packages:

• AffyCompatible
• BAC
• BitSeq
• BrainSABER
• bridge
• cellTree
• ctgGEM
• coexnet
• conclus
• CytoTree
• DEComplexDisease
• flowUtils
• flowCL
• gaia
• gpart
• inveRsion
• IsoGeneGUI
• iteremoval
• MACPET
• PoTRA
• rama
• Rcade
• RNASeqR
• scAlign
• scMAGeCK
• sojourner
• TCGAbiolinksGUI
• TDARACNE
• TimeSeriesExperiment
• TraRe
• tspair
• XCIR

Experiment Data Packages:

• gatingMLData
• RNASeqRData

Software Packages:

• ABAEnrichment
• Autotuner
• CAnD
• caOmicsV
• clonotypeR
• CountClust
• diffloop
• GCSConnection
• GCSFilesystem
• GenoGAM
• genphen
• gprege
• networkBMA
• Onassis
• perturbatr
• ppiStats
• ProteomicsAnnotationHubData
• PSICQUIC
• PubScore
• Rgin
• RmiR
• RpsiXML
• ScISI
• SLGI
• Sushi
• tofsims
• TSRchitect

Experiment Data Packages:

• DREAM4
• MSstatsBioData
• ppiData

Workflow Packages:

• proteomics

Annotation Packages:

• MafH5.gnomAD.v3.1.1.GRCh38_3.13.1.tar.gz
• SNPlocs.Hsapiens.dbSNP.20101109
• SNPlocs.Hsapiens.dbSNP.20120608
• SNPlocs.Hsapiens.dbSNP141.GRCh38
• SNPlocs.Hsapiens.dbSNP142.GRCh37
• SNPlocs.Hsapiens.dbSNP151.GRCh38
• XtraSNPlocs.Hsapiens.dbSNP141.GRCh38

Software Packages:

• affyPara
• ALPS
• alsace
• BrainStars
• dualKS
• ENCODExplorer
• ENVISIONQuery
• FindMyFriends
• GeneAnswers
• gramm4R
• KEGGprofile
• MSstatsTMTPTM
• MSGFplus
• MSGFgui
• slinky
• PanVizGenerator
• predictionet
• RGalaxy
• scClassifR
• SRGnet
• SwimR

Experiment Data Packages:

• ABAData
• brainImageRdata
• tcgaWGBSData.hg19

Annotation Packages:

• org.Pf.plasmo.db

Software Packages:

• AffyExpress
• affyQCReport
• AnnotationFuncs
• ArrayTools
• bigmemoryExtras
• BiocCaseStudies
• CancerMutationAnalysis
• ChIPSeqSpike
• CompGO
• CoRegFlux
• CrossICC
• cytofast
• DBChIP
• dexus
• EasyqpcR
• EDDA
• eisa
• ELBOW
• ExpressionView
• FlowRepositoryR
• genoset
• HCABrowser
• HCAExplorer
• HCAMatrixBrowser
• Imetagene
• mdgsa
• metagenomeFeatures
• methyAnalysis
• MSEADbi
• OutlierD
• pcot2
• PCpheno
• Polyfit
• POST
• RchyOptimyx
• RDAVIDWebService
• RNAither
• RNAprobR
• rnaSeqMap
• SAGx
• samExploreR
• seqplots
• simulatorZ
• SSPA
• ToPASeq
• XBSeq
• yaqcaffy

Experiment Data Packages:

• ceu1kg
• ceu1kgv
• ceuhm3
• cgdv17
• dsQTL
• facsDorit
• gskb
• hmyriB36
• JctSeqData
• MAQCsubsetAFX
• yri1kgv

Workflow Packages:

• eQTL

Annotation Data Packages:

• All 12 LRBase.XXX.eg.db packages (replaced with AHLRBaseDbs)
• All 73 MeSH.XXX.eg.db packages (replaced with AHMeSHDbs)
• MafDb.gnomAD.r3.0.GRCh38
• MafH5.gnomAD.r3.0.GRCh38
• greengenes13.5MgDb
• ribosomaldatabaseproject11.5MgDb
• silva128.1MgDb

Software Packages:

• adaptest
• ArrayTV
• BioSeqClass
• CHARGE
• CNVtools
• CorMut
• DESeq (See replacement DESeq2)
• chimera
• explorase
• flowFit
• flowSpy
• flowType
• focalCall
• FourCSeq
• FunciSNP
• GenRank
• GeneticsDesign
• GGBase
• GGtools
• GOFunction
• gQTLBase
• gQTLstats
• hicrep
• ImpulseDE
• ImpulseDE2
• joda
• JunctionSeq
• LINC
• Logolas
• mcaGUI
• metaArray
• metaseqR (see replacement metaseqR2)
• methVisual
• methyvim
• Mirsynergy
• MmPalateMiRNA
• MOFA (see replacement MOFA2)
• MotIV
• NarrowPeaks
• netbenchmark
• netReg
• OGSA
• OmicsMarkeR
• pathprint
• PathwaySplice
• PGA
• PGSEA
• plrs
• prada
• Prize
• Rariant
• reb
• Roleswitch
• rTANDEM
• sapFinder
• scsR
• shinyTANDEM
• sigaR
• signet
• simpleaffy
• spotSegmentation
• Starr
• SVAPLSseq
• TxRegInfra
• xps

Experiment Data Packages:

• flowFitExampleData
• FunciSNP.data
• geuvPack
• geuvStore2
• GGdata
• mitoODEdata
• Mulder2012
• methyvimData
• pathprintGEOData
• pcaGoPromoter.Hs.hg19
• pcaGoPromoter.Mm.mm9
• pcaGoPromoter.Rn.rn4
• waveTilingData
• yriMulti

Software Packages:

• QUALIFIER
• motifRG
• triform
• CVE
• proteoQC
• affypdnn
• splicegear
• Genominator
• IdMappingAnalysis
• IdMappingRetrieval
• manta
• RefNet
• AnalysisPageServer
• scfind
• kimod
• plw
• cobindR
• LMGene
• sRAP
• gCMAP
• gCMAPWeb
• DChIPRep
• CTDquerier
• MTseeker
• readat
• anamiR
• CALIB
• cellGrowth
• chroGPS
• DEDS
• LVSmiRNA
• MCRestimate
• nem
• PAPi
• pcaGoPromoter
• pint
• RIPSeeker
• SANTA
• waveTiling
• BayesPeak
• bgafun
• lol
• M3D
• MergeMaid
• IPPD
• biosvd
• birta
• DupChecker
• FEM
• geecc
• MaxContrastProjection
• mitoODE
• MoPS
• PowerExplorer
• Vega

Experiment Data Packages:

• MTseekerData
• RIPSeekerData

Annotation Data Packages:

• hom.At.inp.db
• hom.Ce.inp.db
• hom.Dm.inp.db
• hom.Dr.inp.db
• hom.Hs.inp.db
• hom.Mm.inp.db
• hom.Rn.inp.db
• hom.Sc.inp.db
• KEGG.db(use KEGGREST instead)
• MafDb.ESP6500SI.V2.SSA137.hs37d5
• MafDb.EXP6500SI.V2.SSA137.GRCh38

Software Packages:

• SNPchip
• GenomeGraphs
• HTSanalyzeR
• Rchemcpp
• charm
• Pbase
• dSimer
• flipflop
• exomePeak
• CNPBayes
• brainImageR
• plateCore
• rHVDM
• SEPA
• condcomp
• birte
• mlm4omics
• RnaSeqSampleSize
• CAMTHC (renamed to debCAM)

Experiment Data Packages:

• charmData
• facopy.annot
• allenpvc

Annotation Data Packages:

• MafDb.gnomADex.r2.0.1.GRCh38 (replaced with MafDb.gnomADex.r2.1.GRCh38)
• MafDb.gnomAD.r2.0.1.GRCh38 (replaced witht MafDb.gnomAD.r2.1.GRCh38)
• MafDb.gnomADex.r2.0.1.hs37d5 (replaced with MafDb.gnomADex.r2.1.hs37d5)
• MafDb.gnomAD.r2.0.1.hs37d5 (replaced with MafDb.gnomAD.r2.1.hs37d5)
• MafDb.ESP6500SI.V2.SSA137.hs37d5
• MafDb.EXP6500SI.V2.SSA137.GRCh38

Software Packages:

• flowQ
• flowQB
• ProCoNA
• htSeqTools
• rMAT
• TSSi
• NGScopy
• spliceSites
• SVM2CRM
• rSFFreader
• DOQTL
• miRsponge (renamed to miRspongeR)

Experiment Data Packages:

• PGPC
• flowQBData

Software Packages:

• ampliQueso
• BiocInstaller (Replaced by BiocManager)
• cytofkit
• facopy
• gaucho
• GeneSelector
• GoogleGenomics
• IrisSpatialFeatures
• mQTL.NMR
• nudge
• pbcmc
• prot2D
• RamiGO

Experiment Data Packages:

• iontreeData
• MSBdata (Renamed to MSMB)

Software Packages:

• BrowserVizDemo
• DASC
• mvGST
• ontoCAT
• OperaMate
• PAnnBuilder
• phenoDist
• spliceR

Experiment Data Packages:

• cheung2010
• MEALData
• RnaSeqTutorial

Software Packages:

• BioMedR
• ddgraph
• domainsignatures
• EWCE
• HCsnip
• oneChannelGUI
• stepwiseCM
• iontree
• RCytoscape

Annotation Data Packages:

• IlluminaHumanMethylation450k.db

Software Packages:

• AtlasRDF
• CopyNumber450k
• coRNAi
• GENE.E
• GEOsearch
• MeSHEim
• mmnet
• pdmclass
• saps

Experimental Data Packages:

• CopyNumber450kData

Software Packages:

• betr

Experimental Data Packages:

• encoDnaseI
• ggtut

Annotation Packages:

• gahgu133a.db
• gahgu133acdf
• gahgu133aprobe
• gahgu133b.db
• gahgu133bcdf
• gahgu133bprobe
• gahgu133plus2.db
• gahgu133plus2cdf
• gahgu133plus2probe
• gahgu95av2.db
• gahgu95av2cdf
• gahgu95av2probe
• gahgu95b.db
• gahgu95bcdf
• gahgu95bprobe
• gahgu95c.db
• gahgu95ccdf
• gahgu95cprobe
• gahgu95d.db
• gahgu95dcdf
• gahgu95dprobe
• gahgu95e.db
• gahgu95ecdf
• gahgu95eprobe
• IlluminaHumanMethylation450k.db
• org.Sco.eg.db.html
• org.Tgondii.eg.db

Software Packages:

• AffyTiling
• cellHTS
• DASiR
• DAVIDQuery
• GenoView
• inSilicoDb
• inSilicoMerging
• jmosaic
• metaX
• MMDiff
• neaGUI
• Rolexa
• RWebServices
• SJava
• SomaticCA
• spade

Experimental Data Packages:

• geuvStore
• ind1KG

No packages were removed with this release. 17 packages were marked as deprecated, to be removed in the next release.

No packages were removed with this release.

• asmn
• COPDSexualDimorphism
• DNaseR
• flowFlowJo
• flowPhyto

• RMAPPER
• virtualArray

• Agi4x44PreProcess
• maDB
• pgUtils

• dualKS
• externalVector
• GeneGroupAnalysis
• iFlow
• KEGGSOAP
• xmapcore

• cosmo
• cosmoGUI
• gene2pathway

• PatientGeneSets

• edd
• GeneRfold
• ontoTools
• GeneR
• RMAGEML
• RTooks4TB

• GeneSpring
• GeneTraffic
• makePlatformDesign
• Rdbi
• RdbiPgSQL
• rflowcyt
• Rredland
• Ruuid
• simulatorAPMS
• snpMatrix

• exonmap
• biocDatasets

• matchprobes
• GeneticsBase
• fbat

• keggorth was renamed to keggorthology.

• stam
• Rintact

• AnnBuilder
• RSNPer

• SemSim
• WidgetInvoke

• SAGElyzer
• GeneTS
• arrayMagic
• chromoViz
• iSPlot
• iSNetword

• bim
• arrayQCplot

• gff3Plotter
• mmgmos
• applera

• reposTools
• exprExternal
• SNAData
• rfcdmin
• goCluster
• GenomeBase
• y2hStat

• msbase
• ideogram

• mscalib

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