Removed Packages
A list of packages removed from Bioconductor along with their last-available landing pages.
Packages deprecated in Bioconductor 3.21 (to be removed in 3.22)
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:
Annotation Data Packages:
Workflow Packages:
Packages removed with Bioconductor 3.21 release
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:
Packages removed with Bioconductor 3.20 release
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:
Packages removed with Bioconductor 3.19 release
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:
Packages removed with Bioconductor 3.18 release
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:
Packages removed with Bioconductor 3.17 release
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:
Packages removed with Bioconductor 3.16 release
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:
Workflow Packages:
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
Packages removed with Bioconductor 3.15 release
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:
Annotation Packages:
Packages removed with Bioconductor 3.14 release
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:
Workflow Packages:
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
Packages removed with Bioconductor 3.13 release
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
Packages removed with Bioconductor 3.12 release
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:
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
Packages removed with Bioconductor 3.11 release
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:
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
Packages removed with Bioconductor 3.10 release
Software Packages:
- flowQ
- flowQB
- ProCoNA
- htSeqTools
- rMAT
- TSSi
- NGScopy
- spliceSites
- SVM2CRM
- rSFFreader
- DOQTL
- miRsponge (renamed to miRspongeR)
Experiment Data Packages:
Packages removed with Bioconductor 3.9 release
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)
Packages removed with Bioconductor 3.8 release
Software Packages:
Experiment Data Packages:
Packages removed with Bioconductor 3.7 release
Software Packages:
Annotation Data Packages:
Packages removed with Bioconductor 3.6 release
Software Packages:
Experimental Data Packages:
Packages removed with Bioconductor 3.5 release
Software Packages:
Experimental Data Packages:
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
Packages removed with Bioconductor 3.4 release
Software Packages:
- AffyTiling
- cellHTS
- DASiR
- DAVIDQuery
- GenoView
- inSilicoDb
- inSilicoMerging
- jmosaic
- metaX
- MMDiff
- neaGUI
- Rolexa
- RWebServices
- SJava
- SomaticCA
- spade
Experimental Data Packages:
Packages removed with Bioconductor 3.3 release
No packages were removed with this release. 17 packages were marked as deprecated, to be removed in the next release.
Packages removed with Bioconductor 3.2 release
No packages were removed with this release.
Packages removed with Bioconductor 3.1 release
Packages removed with Bioconductor 3.0 release
Packages removed with Bioconductor 2.14 release
Packages removed with Bioconductor 2.13 release
Packages removed with Bioconductor 2.12 release
Packages removed with Bioconductor 2.11 release
Packages removed with Bioconductor 2.10 release
Packages removed with Bioconductor 2.9 release
- GeneSpring
- GeneTraffic
- makePlatformDesign
- Rdbi
- RdbiPgSQL
- rflowcyt
- Rredland
- Ruuid
- simulatorAPMS
- snpMatrix
Packages removed with Bioconductor 2.8 release
Packages removed with Bioconductor 2.7 release
Packages removed with Bioconductor 2.6 release
- keggorth was renamed to keggorthology.
Packages removed with Bioconductor 2.5 release
Packages removed with Bioconductor 2.4 release
Packages removed with Bioconductor 2.3 release
Packages removed with Bioconductor 2.2 release
Packages removed with Bioconductor 2.1 release
Packages removed with Bioconductor 2.0 release
Packages removed with Bioconductor 1.9 release
Packages removed with Bioconductor 1.8 release
- msbase
- ideogram
Packages removed with Bioconductor 1.7 release
- mscalib