Uppsala Multidisciplinary Center for Advanced Computational Science

R_PACKAGES/3.5.0

The following R packages are available as part of the R_packages/3.5.0 module as installed on rackham, irma and bianca, which requires and loads the R/3.5.0 module.  When the R_packages/3.5.0 module is loaded, it adds a directory to the R_LIBS_SITE environment variable.  Within R, these packages will be available via library(package-name).

Note the list of package names is sorted case-insensitive.

PackageVersion
A31.0.0
a41.28.0
a4Base1.28.0
a4Classif1.28.0
a4Core1.28.0
a4Preproc1.28.0
a4Reporting1.28.0
ABAData1.10.0
ABAEnrichment1.10.0
ABarray1.48.0
abbyyR0.5.4
abc2.1
abc.data1.0
ABC.RAP0.9.0
ABCanalysis1.2.1
ABCoptim0.15.0
ABCp21.2
abcrf1.7.1
abctools1.1.3
abd0.2-8
abe3.0.1
abf20.7-1
ABHgenotypeR1.0.1
abind1.4-5
abjutils0.2.1
abn1.0.2
abnormality0.1.0
abodOutlier0.1
ABPS0.2
AbsFilterGSEA1.5.1
AbSim0.2.4
ABSSeq1.34.1
abundant1.1
Ac3net1.2.2
ACA1.1
acc1.3.3
accelerometry2.2.5
accelmissing1.4
AcceptanceSampling1.0-5
ACCLMA1.0
accrual1.3
accrued1.4.1
accSDA1.0.0
ACD1.5.3
acde1.10.0
ACDm1.0.4
acebayes1.5
acepack1.4.1
ACEt1.8.0
aCGH1.58.0
acid1.1
acm4r1.0
ACME2.36.0
ACMEeqtl1.6
acmeR1.1.0
ACNE0.8.1
acnr1.0.0
acopula0.9.2
acp2.1
aCRM0.1.1
AcrossTic1.0-3
acrt1.0.1
acs2.1.3
ACSNMineR0.16.8.25
acss0.2-5
acss.data1.0
ACSWR1.0
ACTCD1.2-0
Actigraphy1.3.2
ActiveDriver1.0.0
activity1.1
activpalProcessing1.0.2
actogrammr0.2.3
actuar2.3-1
AcuityView0.1
ada2.0-5
adabag4.2
ADaCGH22.20.0
adagio0.7.1
AdapEnetClass1.2
adapr2.0.0
AdapSamp1.1.1
adaptest1.0.0
AdaptFit0.2-2
AdaptFitOS0.67
AdaptGauss1.3.5
adaptiveGPCA0.1.2
AdaptiveSparsity1.5
adaptivetau2.2-1
adaptMCMC1.3
adaptsmoFMRI1.1
adaptTest1.0
ADCT0.1.0
addhaz0.4
addhazard1.1.0
addinslist0.2
additiveDEA1.1
additivityTests1.1-4
addreg3.0
ADDT2.0
ade41.7-11
ade4TkGUI0.2-9
adeba1.1.2
adegenet2.1.1
adegraphics1.0-10
adehabitatHR0.4.15
adehabitatHS0.3.13
adehabitatLT0.3.23
adehabitatMA0.3.12
adephylo1.1-11
adepro2.0.0
AdequacyModel2.0.0
adespatial0.2-0
adfExplorer0.1.4
ADGofTest0.3
AdhereR0.2.0
adhoc1.1
adimpro0.8.2
adiv1.1
AdjBQR1.0
adjclust0.5.6
adjustedcranlogs0.1.0
adklakedata0.6.1
adlift1.4-1
ADM31.3
adme16cod.db3.4.0
AdMit2.1.3
admixturegraph1.0.2
ADMM0.3.0
ADMMnet0.1
ADMMsigma2.0
adnuts1.0.0
ADPclust0.7
ADPF0.0.1
ads1.5-3
adSplit1.50.0
AdvBinomApps1.0
advclust0.4
AdvDif40.2.18
adwave1.3
aemo0.2.0
AER1.2-5
AF0.1.4
afc1.4.0
afCEC1.0.2
afex0.21-2
affluenceIndex1.0
affxparser1.52.0
affy1.58.0
affycomp1.56.0
AffyCompatible1.40.0
affycompData1.18.0
affyContam1.38.0
affycoretools1.52.1
affydata1.28.0
AffyExpress1.46.0
Affyhgu133A2Expr1.16.0
Affyhgu133aExpr1.18.0
Affyhgu133Plus2Expr1.14.0
affyILM1.32.0
affyio1.50.0
affylmGUI1.54.1
AffymetrixDataTestFiles0.18.0
Affymoe4302Expr1.18.0
affyPara1.40.0
affypdnn1.54.0
affyPLM1.56.0
affyQCReport1.58.0
AffyRNADegradation1.26.0
AFLPsim0.4-2
AFM1.2.4
afmToolkit0.0.1
afpt1.0.0
aftgee1.1.3
ag.db3.2.3
agcdf2.18.0
AGD0.39
AGDEX1.28.0
AggregateR0.0.2
aggregation1.0.1
agilp3.12.0
AgiMicroRna2.30.0
agop0.1-4
agprobe2.18.0
Agreement0.8-1
agricolae1.2-8
agridat1.16
agriTutorial0.1.3
agrmt1.40.4
AGSDest2.3.1
agsemisc1.3-1
ahaz1.14
AHCytoBands0.99.0
AHEnsDbs1.0.6
AHMbook0.1.4
ahnr0.3.1
AhoCorasickTrie0.1.0
ahp0.2.12
AHR1.4.2
AICcmodavg2.1-1
AID2.3
aidar1.0.5
AIG0.1.9
AIM1.01
aimPlot1.0.0
AIMS1.12.0
aire.zmvm0.6.1
airGR1.0.10.11
airGRteaching0.2.2.2
airr1.1.0
aiRthermo1.2
airway0.114.0
Ake1.0
akima0.6-2
akmeans1.1
alabama2015.3-1
alakazam0.2.10
albopictus0.3
ald1.2
ALDEx21.12.0
ALDqr1.0
ALEPlot1.1
aLFQ1.3.4
alfred0.1.6
AlgDesign1.1-7.3
AlgebraicHaploPackage1.2
algorithmia0.0.2
algstat0.0.2
AlignStat1.3.1
alineR1.1.4
ALKr0.5.3.1
ALL1.22.0
allan1.01
allanvar1.1
alleHap0.9.9
allelematch2.5
AlleleRetain2.0.2
allelic0.1
AllelicImbalance1.18.0
ALLMLL1.20.0
AllPossibleSpellings1.1
alluvial0.1-2
alphabetr0.2.2
alphahull2.1
alphaOutlier1.2.0
alphashape3d1.3
AlphaVantageClient0.0.1
alphavantager0.1.0
alpine1.6.0
alpineData1.6.0
alr32.0.8
alr41.0.6
ALS0.0.6
alsace1.16.0
ALSCPC1.0
ALSM0.2.0
altcdfenvs2.42.0
alternativeSplicingEvents.hg191.0.1
alternativeSplicingEvents.hg381.0.1
alterryx0.3.1
altmeta2.2
ALTopt0.1.1
amap0.8-16
AMAP.Seq1.0
AMCP0.0.4
AMCTestmakeR0.1.0
ameco0.2.9
amei1.0-7
Amelia1.7.5
amelie0.2.0
amen1.3
AmericanCallOpt0.95
AmesHousing0.0.3
AMGET1.0
AMIAS1.0.2
AmigaFFH0.1.2
aml0.1-1
AMModels0.1.3
AmmoniaConcentration0.1
aMNLFA0.1
AMOEBA1.1
AMORE0.2-15
AMOUNTAIN1.6.0
AmpAffyExample1.20.0
ampd0.2
amplican1.2.1
AmpliconDuo1.1
ampliQueso1.18.0
AMR0.2.0
amt0.0.4.0
AmyloGram1.1
AnaCoDa0.1.1
anacor1.1-3
analogsea0.6.0
analogue0.17-0
analogueExtra0.1-1
AnalysisPageServer1.14.0
analytics2.0
analyz1.4
AnalyzeFMRI1.1-17
AnalyzeTS2.2
anamiR1.8.0
Anaquin2.4.0
AncestryMapper2.0
anchoredDistr1.0.3
anchors3.0-8
AnDE1.0
andrews1.0
anesrake0.80
AneuFinder1.8.0
AneuFinderData1.8.0
ANF1.2.0
anfis0.99.1
AnglerCreelSurveySimulation1.0.2
aniDom0.1.3
anim.plots0.2
animalTrack1.0.0
animation2.5
ANLP1.3
anMC0.2.1
ANN21.5
annaffy1.52.0
annmap1.22.0
annotate1.58.0
annotation1.2.0
AnnotationBustR1.2
AnnotationDbi1.42.1
AnnotationFilter1.4.0
AnnotationForge1.22.1
AnnotationFuncs1.30.0
AnnotationHub2.12.0
AnnotationHubData1.10.1
annotationTools1.54.0
annotatr1.6.0
AnnotLists1.2
annovarR1.0.0
AnnuityRIR1.0-0
anocva0.1.1
anoint1.4
ANOM0.5
anomalyDetection0.2.5
anominate0.6
anonymizer0.2.0
anopheles.db03.6.0
anota1.28.0
anota2seq1.2.0
ANOVA.TFNs1.0
ANOVAreplication1.1.3
AntAngioCOOL1.2
antaresProcessing0.15.3
antaresRead2.1.2
Anthropometry1.10
antiProfiles1.20.0
antiProfilesData1.16.0
antitrust0.99.10
antiword1.1
AntWeb0.7
anytime0.3.1
aod1.3
aods30.4-1
aoos0.5.0
aop1.0.0
Aoptbdtvc0.0.2
apa0.2.0
apaStyle0.5
apaTables2.0.4
apaText0.1.1
apc1.3
APCanalysis1.0
apcluster1.4.7
apComplex2.46.0
apdesign1.0.0
ape5.1
apeglm1.2.0
apercu0.2.3
apex1.0.3
aphid1.1.0
aplore30.9
aplpack1.3.2
APML00.9
apmsWAPP1.0
apng1.0
appell0.0-4
APPEstimation0.1.1
apple0.3
AppliedPredictiveModeling1.1-7
appnn1.0-0
approximator1.2-6
approxmatch1.0
aprean31.0.1
apricom1.0.0
aprof0.4.1
APSIM0.9.2
APSIMBatch0.1.0.2374
apsimr1.2
apsrtable0.8-8
apt2.5
aptg0.1.0
APtools5.1
apTreeshape1.5-0
aqfig0.8
aqp1.16
aqr0.4
AquaEnv1.0-4
AR1.1
AR1seg1.0
arabicStemR1.2
arabidopsis.db03.6.0
aracne.networks1.6.0
ArArRedux0.2
arc1.2
ARCensReg2.1
archdata1.2
archetypes2.2-0
archiDART3.2
archivist2.3.1
archivist.github0.2.2
ArCo0.3-1
ArDec2.0
areaplot1.2-0
arf3DS42.5-10
arfima1.6-7
ArfimaMLM1.3
argon20.2-0
argosfilter0.63
argparse1.1.1
argparser0.4
ArgumentCheck0.10.2
ARHT0.1.0
ari0.1.0
aricode0.1.1
arm1.10-1
arnie0.1.2
aroma.affymetrix3.1.1
aroma.apd0.6.0
aroma.cn1.6.1
aroma.core3.1.3
aroma.light3.10.0
Arothron1.0.2
ARPobservation1.1
aRpsDCA1.1.1
arrangements1.0.2
arrApply2.0.1
ArrayBin0.2
ArrayExpress1.40.0
ArrayExpressHTS1.30.0
arrayhelpers1.0-20160527
arrayMvout1.38.0
arrayQuality1.58.0
arrayQualityMetrics3.36.0
arrays1.4.0
ArrayTools1.40.0
ArrayTV1.18.0
ARRmData1.16.0
ARRmNormalization1.20.0
ars0.5
arsenal1.3.0
ART1.0
artfima1.5
ARTIVA1.2.3
ARTool0.10.5
ARTP2.0.5
ARTP20.9.32
arules1.6-1
arulesCBA1.1.3-1
arulesNBMiner0.1-5
arulesSequences0.2-19
arulesViz1.3-1
aRxiv0.5.16
as.color0.1
ASAFE1.6.0
asaur0.50
asbio1.5-2
ASCAT2.5.1
ascii2.1
asciiruler0.2
asciiSetupReader1.4.0
asd2.2
asdreader0.1-3
ASEB1.24.0
ASGS.foyer0.2.1
ASGSCA1.14.0
ash1.0-15
AshkenazimSonChr211.10.0
ashr2.2-7
asht0.9.3
ASICS1.0.0
ASICSdata1.0.0
AsioHeaders1.11.0-1
aslib0.1
ASMap1.0-2
asnipe1.1.10
aspace3.2
ASPBay1.2
aSPC0.1.2
aspect1.0-5
aspi0.2.0
ASpli1.6.0
aSPU1.48
asremlPlus2.0-12
ASSA1.0
AssayCorrector2.0.0
assertable0.2.4
assertive0.3-5
assertive.base0.0-7
assertive.code0.0-1
assertive.data0.0-1
assertive.data.uk0.0-1
assertive.data.us0.0-1
assertive.datetimes0.0-2
assertive.files0.0-2
assertive.matrices0.0-1
assertive.models0.0-1
assertive.numbers0.0-2
assertive.properties0.0-4
assertive.reflection0.0-4
assertive.sets0.0-3
assertive.strings0.0-3
assertive.types0.0-3
assertr2.5
assertthat0.2.0
ASSET1.98.0
AssetPricing1.0-1
ASSIGN1.16.0
assignPOP1.1.4
assist3.1.3
ASSISTant1.2-3
AssocAFC1.0.2
assocInd1.0.1
AssocTests0.0-4
assortnet0.12
AssotesteR0.1-10
aster1.0-2
aster20.3
astro1.2
astrochron0.8
astrodatR0.1
astroFns4.1-0
astrolibR0.1
astsa1.8
asus1.0.0
asVPC1.0.2
asymLD0.1
asympTest0.1.4
AsynchLong2.0
asypow2015.6.25
ATACseqQC1.4.2
ATE0.2.0
AtelieR0.24
ath1121501.db3.2.3
ath1121501cdf2.18.0
ath1121501probe2.18.0
atmcmc1.0
ATmet1.2
AtmRay1.31
ATR0.1-0
aTSA3.1.2
atsd1.2.0
attempt0.2.1
attract1.32.0
attrCUSUM0.1.0
attribrisk0.1
atus0.1
AUC0.3.0
AUCell1.2.4
aucm2018.1-24
AUCRF1.1
auctestr1.0.0
audio0.1-5.1
audiolyzR0.4-9
audit0.1-1
auditor0.2.1
augSIMEX2.2
auk0.2.2
aurelius0.8.4
AurieLSHGaussian0.2.0
AUtests0.98
auto.pca0.3
autoBagging0.1.0
AutoDeskR0.1.3
autoencoder1.1
autoFRK1.0.0
autoimage2.0
automagic0.3
automap1.0-14
AutoModel0.4.9
automultinomial1.0.0
autoplotly0.1.2
Autoplotprotein1.1
autopls1.3
AutoregressionMDE1.0
AutoSEARCH1.5
autoSEM0.1.0
autothresholdr1.2.1
autovarCore1.0-4
available1.0.1
averisk1.0.3
aVirtualTwins1.0.1
AWR1.11.189
AWR.Athena1.1.0-1
AWR.Kinesis1.7.3
AWR.KMS0.1
aws1.9-6
aws.alexa0.1.6
aws.cloudtrail0.1.5
aws.comprehend0.1.2
aws.ec2metadata0.1.5
aws.iam0.1.7
aws.lambda0.1.6
aws.polly0.1.2
aws.s30.3.12
aws.ses0.1.4
aws.signature0.4.1
aws.sns0.1.7
aws.sqs0.1.10
aws.transcribe0.1.2
aws.translate0.1.3
awsjavasdk0.2.0
awsMethods1.1-0
awspack0.1.6
AzureML0.2.14
B2Z1.4
b6e6rl1.1
BaalChIP1.6.0
babar1.0
babel0.3-0
BaBooN0.2-0
babynames0.3.0
BAC1.40.0
BACA1.3
BACCO2.0-9
backblazer0.1.0
backpipe0.2.3
backports1.1.2
backShift0.1.4.2
backtest0.3-4
bacon1.8.0
BACprior2.0
bacr1.0.1
BADER1.18.0
badgecreatr0.1.0
badger0.0.2
BadRegionFinder1.8.0
BAEssd1.0.1
Bagidis1.0
bagRboostR0.0.2
BAGS2.20.0
bairt0.1.2
baitmet1.0.1
BalanceCheck0.1
BalancedSampling1.5.2
BALCONY0.2.8
Ball1.2.0
ballgown2.12.0
ballr0.2.1
BaM1.0.1
BAMBI2.0.1
bamlss1.0-0
BAMMtools2.1.6
bamsignals1.12.1
bandit0.5.0
BANEScarparkinglite0.1.2
bang1.0.0
bannerCommenter0.1.0
banocc1.4.0
banR0.2.0
banxicoR0.9.0
bapred1.0
BaPreStoPro0.1
BarBorGradient1.0.5
barcode1.1
BarcodingR1.0-2
barley1cdf2.18.0
barley1probe2.18.0
Barnard1.8
BART1.8
bartMachine1.2.4.2
bartMachineJARs1.1
Barycenter1.3.1
BAS1.5.1
basad0.2.0
base2grob0.0.3
base642.0
base64enc0.1-3
base64url1.4
baseballDBR0.1.2
basecallQC1.4.0
basefun1.0-1
baseline1.2-1
BaseSpaceR1.24.0
Basic4Cseq1.16.0
BASiCS1.2.1
basicspace0.20
BasicSTARRseq1.8.0
basictabler0.1.0
basicTrendline2.0.3
BASiNET0.0.3
BASIX1.1
BASS0.2.2
BaSTA1.9.4
bastah1.0.7
BAT1.5.6
batade0.1
batch1.1-5
BatchExperiments1.4.2
BatchGetSymbols2.1
BatchJobs1.7
BatchMap1.0.2.0
batchmeans1.0-3
BatchQC1.8.0
batchtools0.9.10
BaTFLED3D0.2.11
batman0.1.0
batteryreduction0.1.1
BAwiR1.1.1
BayClone21.1
bayesAB1.1.1
bayesammi0.1.0
BayesBD1.2
BayesBinMix1.4.1
bayesbio1.0.0
bayesboot0.2.2
BayesCombo1.0
BayesComm0.1-2
BayesCR2.1
BayesDA2012.04-1
bayesDccGarch2.0
BAYESDEF0.1.0
bayesDem2.5-1
bayesDP1.3.2
BayesESS0.1.12
BayesFactor0.9.12-4.2
BayesFM0.1.2
bayesGARCH2.1.3
bayesGDS0.6.2
BayesGESM1.4
BayesGOF4.0
BayesH1.0
BayesianAnimalTracker1.2
Bayesianbetareg1.2
bayesianETAS1.0.3
BayesianGLasso0.2.0
BayesianNetwork0.1.3
BayesianTools0.1.5
bayesImageS0.5-2
BayesKnockdown1.6.0
BayesLCA1.7
bayesLife3.2-0
bayeslm0.8.0
bayesloglin1.0.1
bayeslongitudinal0.1.0
bayesLopod1.0.1
bayesm3.1-0.1
BayesMAMS0.1
bayesmeta2.2
BayesMixSurv0.9.1
BayesNI0.1
BayesPeak1.32.0
BayesPieceHazSelect1.1.0
BayesPiecewiseICAR0.2.1
bayesplot1.5.0
bayesPop6.2-4
bayespref1.0
bayesQR2.3
bayess1.4
BayesS51.30
BayesSAE1.0-2
BayesSingleSub0.6.2
BayesSpec0.5.3
BayesSummaryStatLM1.0-1
bayesSurv3.2
bayesTFR6.1-2
Bayesthresh2.0.1
BayesTree0.3-1.4
BayesTreePrior1.0.1
BayesValidate0.0
BayesVarSel1.8.0
BayesX0.3-0
BayesXsrc3.0-1
BayHap1.0.1
BayHaz0.1-3
BaylorEdPsych0.5
bayou2.1
baySeq2.14.0
baystability0.1.0
BAYSTAR0.2-9
bazar1.0.6
BB2014.10-1
BBCAnalyzer1.10.0
bbefkr4.2
bbemkr2.0
BBEST0.1-6
BBmisc1.11
bbmle1.0.20
BBMM3.0
BBMV2.1
bbo0.2
BBRecapture0.1
bbw0.1.3
bc3net1.0.4
BCA0.9-3
BCBCSF1.0-1
BCC19970.1.1
BCDating0.9.7
BcDiag1.0.10
BCE2.1
BCEA2.2-6
BCEE1.2
BCellMA0.3.4
bcellViper1.16.0
bcgam1.0
BCgee0.1
Bchron4.3.0
Bclim3.1.2
bclust1.5
BClustLonG0.1.2
bcp4.0.2
bcpa1.1
bcpmeta1.0
BCRA2.0
BCRANK1.42.0
bcRep1.3.6
bcrm0.4.7
bcROCsurface1.0-2
bcrypt1.1
bcSeq1.2.0
BCSub0.5
bcv1.0.1
bda10.1.9
bde1.0.1
BDgraph2.51
bdlp0.9-1
bdots0.1.19
bdpv1.1
bdscale2.0.0
bdsmatrix1.3-3
bdvis0.2.20
BDWreg1.2.0
bdynsys1.3
bea.R1.0.6
BEACH1.2.1
beachmat1.2.1
beadarray2.30.0
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RcmdrPlugin.EZR1.37
RcmdrPlugin.FactoMineR1.6-0
RcmdrPlugin.FuzzyClust1.1
RcmdrPlugin.GWRM1.0.2
RcmdrPlugin.HH1.1-47
RcmdrPlugin.IPSUR0.2-1
RcmdrPlugin.KMggplot20.2-5
RcmdrPlugin.lfstat0.8.3
RcmdrPlugin.MA0.0-2
RcmdrPlugin.mosaic1.0-7
RcmdrPlugin.MPAStats1.2.2
RcmdrPlugin.NMBU1.8.8
RcmdrPlugin.OptimClassifier0.1.2
RcmdrPlugin.orloca4.6
RcmdrPlugin.PcaRobust1.1.4
RcmdrPlugin.plotByGroup0.1-0
RcmdrPlugin.pointG0.6.6
RcmdrPlugin.qual2.2.6
RcmdrPlugin.ROC1.0-18
RcmdrPlugin.sampling1.1
RcmdrPlugin.SCDA1.1
RcmdrPlugin.SLC0.2
RcmdrPlugin.SM0.3.1
RcmdrPlugin.sos0.3-0
RcmdrPlugin.steepness0.3-2
RcmdrPlugin.survival1.2-0
RcmdrPlugin.TeachingDemos1.1-0
RcmdrPlugin.temis0.7.10
RcmdrPlugin.UCA4.2-4
RCMIP51.2.0
Rcolombos2.0.2
RColorBrewer1.1-2
rcompanion1.13.2
rcongresso0.4.6
RConics1.0
rcorpora2.0.0
Rcpi1.16.2
RCPmod2.186
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Rcpp113.1.2.0
RcppAlgos2.0.3
RcppAnnoy0.0.10
RcppArmadillo0.8.600.0.0
RcppBDT0.2.3
RcppBlaze0.2.2
RcppCCTZ0.2.3
RcppClassic0.9.11
RcppClassicExamples0.1.2
RcppCNPy0.2.9
RcppCWB0.2.4
RcppDE0.1.6
RcppDL0.0.5
RcppEigen0.3.3.4.0
RcppExamples0.1.8
RcppFaddeeva0.1.0
RcppGetconf0.0.2
RcppGreedySetCover0.1.0
RcppGSL0.3.6
RcppHMM1.2.2
RcppHoney0.1.7
RcppMLPACK1.0.10-6
RcppMsgPack0.2.2
RcppNumerical0.3-2
RcppParallel4.4.1
RcppProgress0.4.1
RcppQuantuccia0.0.2
RcppRoll0.3.0
RcppSMC0.2.1
RcppStreams0.1.1
RcppThread0.4.0
RcppTN0.2-2
RcppTOML0.1.3
RcppXPtrUtils0.1.0
RcppXts0.0.4
RcppZiggurat0.1.5
rcqp0.5
Rcrawler0.1.7-0
rcreds0.6.6
RCriteo1.0.2
Rcriticor2.0
RCRnorm0.0.2
rcrossref0.8.0
rcrypt0.1.1
RCrypto0.1.0
Rcsdp0.1.55
rcss1.2
Rcssplot0.3.0
rcube0.2
rCUR1.3
rcure0.1.0
RCurl1.95-4.11
rcv0.2.1
RCy32.0.86
RCyjs2.2.2
Rd2md0.0.2
Rd2roxygen1.6.2
rda1.0.2-2.1
RDataCanvas0.1
rdatacite0.4.0
rdatamarket0.6.5
rdataretriever1.0.0
RDAVIDWebService1.18.0
rdd0.57
rddapp1.1.0
rddensity0.2.2
rddtools0.4.0
rdetools1.0
rdfp0.1.2
rDGIdb1.6.0
rdi1.0.0
rdian0.1.1
Rdice1.0.0
RDIDQ1.0
Rdimtools0.3.2
Rdisop1.40.0
rdist0.0.3
Rdistance1.3.2
rdiversity1.2.1
rdlocrand0.3
RDML0.9-9
rdmulti0.2
rDNAse1.1-1
rdnb0.1-1
RDocumentation0.8.2
RDota20.1.6
rDotNet0.9.1
rdoxygen1.0.0
Rdpack0.8-0
rdpla0.2.0
rdpower0.2
rdrobust0.99.3
Rdrools1.1.0
Rdroolsjars1.0.1
rdrop20.8.1
RDRToolbox1.30.0
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RDS0.8-1
Rdsdp1.0.4-2
Rdsm2.1.1
RDSTK1.1
RDStreeboot1.0
Rdtq0.1
Rduino0.1
rDVR0.1.1
rdwd0.10.2
re2r0.2.0
reactome.db1.64.0
reactR0.2.0
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readat1.6.0
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readbulk1.1.0
reader1.0.6
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readit1.0.0
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REAT2.0.0
reb1.58.0
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refGenome1.7.3
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TxDb.Hsapiens.UCSC.hg19.knownGene3.2.2
TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts3.2.2
TxDb.Hsapiens.UCSC.hg38.knownGene3.4.0
TxDb.Mmulatta.UCSC.rheMac3.refGene3.4.3
TxDb.Mmulatta.UCSC.rheMac8.refGene3.4.3
TxDb.Mmusculus.UCSC.mm10.ensGene3.4.0
TxDb.Mmusculus.UCSC.mm10.knownGene3.4.0
TxDb.Mmusculus.UCSC.mm9.knownGene3.2.2
TxDb.Ptroglodytes.UCSC.panTro4.refGene3.4.3
TxDb.Ptroglodytes.UCSC.panTro5.refGene3.4.3
TxDb.Rnorvegicus.BioMart.igis2.3.2
TxDb.Rnorvegicus.UCSC.rn4.ensGene3.2.2
TxDb.Rnorvegicus.UCSC.rn5.refGene3.4.3
TxDb.Rnorvegicus.UCSC.rn6.refGene3.4.3
TxDb.Scerevisiae.UCSC.sacCer2.sgdGene3.2.2
TxDb.Scerevisiae.UCSC.sacCer3.sgdGene3.2.2
TxDb.Sscrofa.UCSC.susScr11.refGene3.4.3
TxDb.Sscrofa.UCSC.susScr3.refGene3.4.3
tximport1.8.0
tximportData1.8.0
txtplot1.0-3
TypeInfo1.46.0
types1.0.0
u133aaofav2cdf2.18.0
u133x3p.db3.2.3
u133x3pcdf2.18.0
u133x3pprobe2.18.0
UBCRM1.0.1
UBL0.0.6
uCAREChemSuiteCLI0.1.2
ucbthesis1.0
ucminf1.1-4
UCR.ColumnNames0.1.0
udapi0.1.1
UdderQuarterInfectionData1.0.0
udpipe0.6
uGMAR2.0.3
uHMM1.0
uiucthemes0.2.0
ukbabynames0.1.1
ukbtools0.11.0
ukgasapi0.14
Ultimixt2.1
Umatrix3.1
ump0.5-8
Umpire1.3.5
umx2.8.0
unbalanced2.0
unbalhaar2.0
UncerIn22.0
UncertainInterval0.4.7
uncertainty0.2.0
UNCLES2.0
uncmbb0.2.0
understandBPMN1.1.0
UNDO1.22.0
UNF2.0.6
unfoldr0.6.5
ungeneanno0.1.6
uniah1.0
Unicode11.0.0-1
uniCox1.0
UniDOE1.0.2
unifDAG1.0.1
unifiedWMWqPCR1.16.0
uniftest1.1
UniIsoRegression0.0-0
UniProt.ws2.20.2
uniqtag1.0
Uniquorn2.0.0
uniReg1.1
unitedR0.3.1
unitizer1.4.5
units0.6-0
unittest1.3-0
univOutl0.1-4
UnivRNG1.1
unix1.3
unjoin0.0.3
unmarked0.12-2
unpivotr0.4.0
unrepx1.0
unrtf1.2
unsystation0.2.0
untb1.7-3
unvotes0.2.0
upclass2.0
uplift0.3.5
UPMASK1.1
UpSetR1.3.3
uptasticsearch0.3.0
uptimeRobot1.0.0
upwaver1.1.0
uqr1.0.0
urca1.3-0
urlshorteneR0.9.2
urltools1.7.0
uroot2.0-9
USAboundaries0.3.1
UScensus2000cdp0.03
UScensus2000tract0.03
UScensus20100.11
USCF0.1.3
usdm1.1-18
usedist0.1.0
useful1.2.5
userfriendlyscience0.7.1
usethis1.3.0
usfertilizer0.1.5
USGSstates2k1.0.1
UsingR2.0-6
uskewFactors2.0
usl1.8.0
usmap0.3.0
uSORT1.6.0
UStatBookABSC1.0.0
ustyc1.0.0
utf81.1.4
utf8latex1.0.4
utility1.4.2
utilsIPEA0.0.6
utiml0.1.4
uuid0.1-2
UWHAM1.0
uwIntroStats0.0.5
vaersNDvax1.0.4
vaersvax1.0.4
vagalumeR0.1.3
valaddin0.1.2
valection1.0.0
validann1.2.1
validate0.2.5
validatejsonr1.0.4
validateRS1.0.0
validatetools0.4.3
valorate1.0-1
valottery0.0.1
valr0.4.1
valuer1.1.2
vanddraabe1.0.0
VanillaICE1.42.4
VAR.etp0.7
varband0.9.0
varbvs2.4-0
vardiag0.2-1
vardpoor0.10.0
VarED1.0.0
VaRES1.0
VarfromPDB2.2.7
varhandle2.0.3
variables1.0-0
VariableScreening0.1.1
varian0.2.2
VarianceGamma0.3-1
variancePartition1.10.0
VariantAnnotation1.26.1
VariantFiltering1.16.0
variants1.2.0
VariantTools1.22.0
VariantToolsData1.4.0
variosig0.1
varrank0.1
VarReg1.0.2
vars1.5-2
VARSEDIG1.7
varSel0.1
VarSelLCM2.1.2
varSelRF0.7-8
VARsignR0.1.3
VarSwapPrice1.0
VARtests1.0.1
vbdm0.0.4
VBLPCM2.4.4
vbmp1.48.0
vbsr0.0.5
VCA1.3.4
vcd1.4-4
vcdExtra0.7-1
vcfR1.8.0
vcov0.0.1
vcr0.1.0
vcrpart1.0-2
VDA1.3
VDAP2.0.0
vdg1.2.0
Vdgraph2.2-2
VdgRsm1.5
vdiffr0.2.3
VDSPCalibration1.0
vec2dtransf1.1
veccompare0.1.0
vecsets1.2.1
VecStatGraphs2D1.8
VecStatGraphs3D1.6
Vega1.28.0
vegalite0.6.1
VegaMC3.18.0
vegan2.5-2
vegan3d1.1-1
vegclust1.7.4
vegdata0.9.1
vegetarian1.2
vembedr0.1.3
venn1.6
VennDiagram1.6.20
venneuler1.1-0
vennLasso0.1.2
vennplot1.0
verification1.42
versions0.3
vertexenum1.0.2
VertexSimilarity0.1
VertexSort0.1-1
VeryLargeIntegers0.1.6
vesselr0.2.1
vetools1.3-28
vetr0.2.5
VetResearchLMM1.0.0
vfcp1.4.0
VGAM1.0-5
VGAMdata1.0-3
VHDClassification0.3
vhica0.2.4
vidger1.0.0
vietnamcode0.1.1
VIF1.0
VIFCP1.2
VIGoR1.0
VIM4.7.0
VIMGUI0.10.0
VineCopula2.1.6
vines1.1.5
violinmplot0.2.1
vioplot0.2
viopoints0.2-1
viper1.14.0
vipor0.4.5
viridis0.5.1
viridisLite0.3.0
virtualspecies1.4-2
virustotal0.2.1
visdat0.5.1
ViSiElse1.2.0
visNetwork2.0.4
visreg2.5-0
vistime0.5.0
visualFields0.5.4
visualize4.3.0
VisuClust1.2
visvow0.1.0
vita1.0.0
vitality1.3
vitisviniferacdf2.18.0
vitisviniferaprobe2.18.0
VizOR0.8-5
vkR0.1
vlad0.1.0
VLF1.0
VLMC1.4-1
vMask1.0
vmd0.1.0
vmsbase2.1.3
VNM7.1
vocaldia0.8.2
vortexR1.1.5
vortexRdata1.0.3
Voss0.1-4
vote1.1-0
voteogram0.2.0
votesys0.1.1
vottrans1.0
vowels1.2-2
vows0.5
voxel1.3.5
VoxR0.5.1
vpc1.0.1
vqtl2.0.4
vrcp0.1.1
vrmlgen1.4.9
VRPM1.2
vrtest0.97
vscc0.2
VSE0.99
vsn3.48.1
vstsr1.0.0
VSURF1.0.4
vtpnet0.20.0
vtreat1.3.0
vudc1.1
vulcan1.2.0
vulcandata1.2.0
VWPre1.1.0
vwr0.3.0
W2CWM2C2.0
W3CMarkupValidator0.1-6
waccR0.1.0
WACS1.0
waffect1.2
waffle0.7.0
wahc1.0
wakefield0.3.3
walkalytics0.1.0
walker0.2.1
walkr0.3.4
walkscoreAPI1.2
wally1.0.9
walmartAPI0.1.5
walrus1.0.3
WARN1.2-3
warpMix0.1.0
washdata0.1.2
wasim1.1.2
waterData1.0.8
waterfall1.0.2
waterfalls0.1.2
wateRmelon1.24.0
WaterML1.7.1
Watersheds1.1
Wats0.10.3
wavClusteR2.14.0
waveband4.7
waved1.2
wavefunction1.0.0
WaveletComp1.1
WaveLetLongMemory0.1.2
wavelets0.3-0
wavemulcor2.2.1
WaverR1.0
waveslim1.7.5
wavethresh4.6.8
waveTiling1.22.0
waveTilingData1.16.0
wBoot1.0.3
wbs1.3
wbstats0.2
wbsts2.0
WCE1.0.1
wCorr1.9.1
WCQ0.2
WDI2.5
weathermetrics1.2.2
weatherr0.1.2
weaver1.46.0
webbioc1.52.0
webchem0.4.0
webdriver1.0.5
WebGestaltR0.1.1
webmockr0.2.6
webp0.4
WebPower0.5
webr0.1.0
webreadr0.4.0
websearchr0.0.2
webshot0.5.0
webTRISr0.1.0
webuse0.1.2
webutils0.6
webvis0.0.2
wec0.4-1
weco1.2
WEE1.0
WeibullR1.0.9
Weighted.Desc.Stat1.0
WeightedCluster1.2-1
WeightedPortTest1.0
weightedScores0.9.5.1
WeightIt0.4.0
weightr1.1.2
weights0.90
weirs0.25
welchADF0.3
WeMix1.0.2
WES.1KG.WUGSC1.12.0
wesanderson0.3.6
wfe1.6
wfg0.1
wfindr0.1.0
wgaim1.4-11
WGCNA1.63
wgeesel1.5
wgsea1.8
WhatIf1.5-9
wheatcdf2.18.0
wheatmap0.1.0
wheatprobe2.18.0
whereport0.1
whisker0.3-2
whitening1.1.0
WhiteStripe2.3.1
WHO0.2
whoami1.1.2
whoapi0.1.2
WhopGenome0.9.7
wicket0.4.0
widals0.5.4
widenet0.1-2
widgetframe0.3.1
widgetTools1.58.0
widyr0.1.1
wiggleplotr1.4.0
wikibooks0.2
WikidataQueryServiceR0.1.1
WikidataR1.4.0
wikilake0.4
WikipediaR1.1
wikipediatrend1.1.14
WikipediR1.5.0
WikiSocio0.7.0
wikitaxa0.2.0
WilcoxCV1.0-2
wildcard1.1.0
wildlifeDI0.2
wildpoker1.1
windex1.0
wingui0.2
winRatioAnalysis0.1.0
wiod0.3.0
wiqid0.1.5
WiSEBoot1.4.0
withr2.1.2
wkb0.3-0
wktmo1.0.5
wle0.9-91
WLreg1.0.0
WMCapacity0.9.6.7
WMDB1.0
wmlf0.1.2
wmtsa2.0-3
wmwpow0.1.0
WMWssp0.3.4
wnl0.4.1
wNNSel0.1
wnominate1.2.5
woe0.2
woeBinning0.1.5
woeR0.1.3
womblR1.0.3
wooldridge1.3.0
word.alignment1.0.9
wordbankr0.3.0
wordcloud2.5
wordcloud20.2.1
wordmatch1.0
wordnet0.1-14
WordPools1.0-2
WordR0.3.1
wordspace0.2-0
workflowr1.1.1
worldmet0.8.4
worm.db03.6.0
worms0.2.2
worrms0.2.8
wosr0.1.1
WPC1.0
wPerm1.0.1
WPKDE0.1
wpp20081.0-1
wpp20101.2-0
wpp20122.2-1
wpp20151.1-0
wpp20171.2-0
wppExplorer2.1-1
wql0.4.9
wqs0.0.1
wrangle0.4
Wrapped2.0
wrapr1.5.1
wrassp0.1.7
WrightMap1.2.1
write.snns0.0-4.2
writexl1.0
WriteXLS4.0.0
WRS20.10-0
wrspathrowData1.0
WRSS1.4
wrswoR1.1
wrswoR.benchmark0.2
wru0.1-7
wskm1.4.28
wsrf1.7.17
wSVM0.1-7
wtest3.1
wTO1.6.1
wtss1.1.0
WufooR0.8
WVPlots1.0.2
wvtool1.0
WWGbook1.0.1
WWR1.2.2
x.ent1.1.7
x121.9.0
x12GUI0.13.0
x13binary1.1.39-1
x3ptools0.0.1
xaringan0.7
xbreed1.0.1
XBRL0.99.18
XBSeq1.12.0
xcms3.2.0
XDE2.26.0
xenopus.db03.6.0
xenopuslaeviscdf2.18.0
xenopuslaevisprobe2.18.0
xergm1.8.2
xergm.common1.7.7
xesreadR0.2.2
xfun0.3
xgboost0.71.2
xgobi1.2-15
XGR1.1.3
xhmmScripts1.1
XHWE1.0
XhybCasneuf1.18.0
XiMpLe0.10-2
xkcd0.0.6
xkcdcolors1.0
XKCDdata0.1.0
xlaevis.db3.2.3
xlaevis2cdf2.18.0
xlaevis2probe2.18.0
XLConnect0.2-15
XLConnectJars0.2-15
xLLiM2.1
xlsimple0.0.1
xlsx0.6.1
xlsxjars0.6.1
xltabr0.1.2
xlutils30.1.0
xmapbridge1.38.0
xmeta1.1-4
Xmisc0.2.1
XML3.98-1.12
xml21.2.0
XML2R0.0.6
xmlparsedata1.0.1
XMRF1.0
xmrr1.0.36
XNomial1.0.4
xoi0.67-4
xplain0.2.1
Xplortext1.1.1
xpose44.6.1
xptr1.1
XR0.7.2
xray0.2
XRJulia0.7.7
XRPython0.8
XRSCC0.1
xseq0.2.1
xslt1.3
xsp0.1.2
xSub0.0.1
xtable1.8-2
xtal1.15
xtermStyle3.0.5
xtractomatic3.4.2
XtraSNPlocs.Hsapiens.dbSNP141.GRCh380.99.12
XtraSNPlocs.Hsapiens.dbSNP144.GRCh370.99.12
XtraSNPlocs.Hsapiens.dbSNP144.GRCh380.99.12
xtropicaliscdf2.18.0
xtropicalisprobe2.18.0
xts0.11-0
xVA0.8.1
XVector0.20.0
xwf0.2-2
xxIRT2.1.0
xyloplot1.6
xyz0.2
yacca1.1
yaImpute1.0-30
yakmoR0.1.1
YaleToolkit4.2.2
yaml2.2.0
yamss1.6.0
YAPSA1.6.0
yaqcaffy1.40.0
yardstick0.0.1
yarn1.6.0
yarrr0.1.5
yasp0.2.0
ycinterextra0.1
ye6100subacdf2.18.0
ye6100subbcdf2.18.0
ye6100subccdf2.18.0
ye6100subdcdf2.18.0
yearn0.1.3
yeast.db03.6.0
yeast2.db3.2.3
yeast2cdf2.18.0
yeast2probe2.18.0
yeastCC1.20.0
yeastExpData0.26.0
yeastGSData0.18.0
yeastNagalakshmi1.16.0
yeastRNASeq0.18.0
yesno0.1.0
ygs98.db3.2.3
ygs98cdf2.18.0
ygs98frmavecs1.3.0
ygs98probe2.18.0
yhat2.0-0
yhatr0.15.1
YieldCurve4.1
ykmeans1.0
yorkr0.0.7
YPInterimTesting0.1.0
YPmodel1.3
yri1kgv0.22.0
yriMulti0.10.0
YuGene1.1.6
yuima1.8.1
yuimaGUI1.2.0
yummlyr0.1.1
zCompositions1.1.1
zeallot0.1.0
ZeBook1.0
zebrafish.db3.2.3
zebrafish.db03.6.0
zebrafishcdf2.18.0
zebrafishprobe2.18.0
zebrafishRNASeq0.114.0
zebu0.1.2
zeitgebr0.3.3
Zelig5.1.6
ZeligChoice0.9-6
ZeligEI0.1-2
zeligverse0.1.1
zendeskR0.4
zenplots0.0-3
zetadiv1.1.1
zfa1.0
zFactor0.1.7
zFPKM1.2.0
ZIBBSeqDiscovery1.0
ZIBseq1.2
zic0.9.1
ZillowR0.1.0
ZIM1.0.3
zinbwave1.2.0
zip1.0.0
zipcode1.0
zipfextR1.0.0
zipfR0.6-10
ziphsmm2.0.6
zlibbioc1.26.0
zoeppritz1.0-7
ZOIP0.1
zoo1.8-3
zooaRch1.2
zoocat0.2.0
zooimage5.5.2
zoom2.0.4
zscorer0.1.0
Zseq0.2.0
zstdr0.1.1
ztable0.2.0
zTree1.0.4
ztype0.1.0
zyp0.10-1

R_packages/3.4.3

The following R packages are available as part of the R_packages/3.4.3 module as installed on rackham, irma and bianca, which requires and loads the R/3.4.3 module.  When the R_packages/3.4.3 module is loaded, it adds a directory to the R_LIBS_SITE environment variable.  Within R, these packages will be available via library(package-name).

Note the list of package names is sorted case-insensitive.

Package Version
abind 1.4-5
acepack 1.4.1
ade4 1.7-10
ade4TkGUI 0.2-9
adegenet 2.1.0
adegraphics 1.0-9
adephylo 1.1-11
affy 1.56.0
affyio 1.48.0
airway 0.112.0
akima 0.6-2
alr4 1.0.5
amap 0.8-14
AMOUNTAIN 1.4.0
annotate 1.56.1
AnnotationDbi 1.40.0
AnnotationFilter 1.2.0
AnnotationForge 1.20.0
AnnotationHub 2.10.1
ape 5.0
apeglm 1.0.3
ArgumentCheck 0.10.2
aroma.light 3.8.0
ASCAT 2.5
ashr 2.0.5
assertthat 0.2.0
backports 1.1.2
base64 2.0
base64enc 0.1-3
BatchJobs 1.7
bayesplot 1.4.0
baySeq 2.12.0
BBmisc 1.11
bbmle 1.0.20
bdsmatrix 1.3-3
beachmat 1.0.2
beadarray 2.28.0
BeadDataPackR 1.30.0
beanplot 1.2
beeswarm 0.2.3
BH 1.65.0-1
BiasedUrn 1.07
bigRR 1.3-10
bindr 0.1
bindrcpp 0.2
Biobase 2.38.0
BiocGenerics 0.24.0
BiocInstaller 1.28.0
BiocParallel 1.12.0
BiocStyle 2.6.1
biocViews 1.46.0
biomaRt 2.34.2
biomformat 1.6.0
Biostrings 2.46.0
biovizBase 1.26.0
bit 1.1-12
bit64 0.9-7
bitops 1.0-6
bladderbatch 1.16.0
blob 1.1.0
bold 0.5.0
bookdown 0.5
brew 1.0-6
brglm 0.6.1
broom 0.4.3
BSgenome 1.46.0
BSgenome.Celegans.UCSC.ce10 1.4.0
BSgenome.Drerio.UCSC.danRer7 1.4.0
BSgenome.Ecoli.NCBI.20080805 1.3.1000
BSgenome.Hsapiens.UCSC.hg19 1.4.0
bsseq 1.14.0
bumphunter 1.20.0
calibrate 1.7.2
car 2.1-6
carData 3.0-0
caret 6.0-78
Category 2.44.0
caTools 1.17.1
ChAMP 2.9.10
ChAMPdata 2.10.0
checkmate 1.8.5
chimeraviz 1.4.3
ChIPpeakAnno 3.12.4
ChIPQC 1.14.0
chipseq 1.28.0
chron 2.3-52
circlize 0.4.3
CircStats 0.2-4
circular 0.4-93
cli 1.0.0
clue 0.3-55
cmprsk 2.2-7
coda 0.19-1
colorspace 1.3-2
colourpicker 1.0
combinat 0.0-8
commonmark 1.4
CompQuadForm 1.4.3
corpcor 1.6.9
corrplot 0.84
covr 3.0.1
cowplot 0.9.2
crayon 1.3.4
crosstalk 1.0.0
crul 0.5.0
csaw 1.12.0
curl 3.1
CVST 0.2-1
cvTools 0.3.2
d3heatmap 0.6.1.1
DAAG 1.22
dada2 1.6.0
data.table 1.10.4-3
DatABEL 0.9-6
DBI 0.7
dbplyr 1.2.0
ddalpha 1.3.1
DDRTree 0.1.5
debugme 1.1.0
DelayedArray 0.4.1
deldir 0.1-14
dendextend 1.6.0
DendSer 1.0.1
densityClust 0.3
DEoptimR 1.0-8
desc 1.1.1
DESeq 1.30.0
DESeq2 1.18.1
deSolve 1.20
destiny 2.6.1
devtools 1.13.4
DEXSeq 1.24.2
dfoptim 2018.2-1
dichromat 2.0-0
DiffBind 2.6.6
digest 0.6.14
dimRed 0.1.0
diptest 0.75-7
DMRcate 1.14.0
DMRcatedata 1.14.0
DNAcopy 1.52.0
doParallel 1.0.11
doRNG 1.6.6
dotCall64 0.9-5.2
dplyr 0.7.4
DRR 0.0.3
DSS 2.26.0
DT 0.2
dtplyr 0.0.2
dygraphs 1.1.1.4
dynamicTreeCut 1.63-1
e1071 1.6-8
ecodist 2.0.1
edgeR 3.20.7
effects 4.0-0
ellipse 0.4.1
emdbook 1.3.9
emojifont 0.5.1
EMT 1.1
EnsDb.Hsapiens.v75 2.99.0
EnsDb.Hsapiens.v79 2.99.0
ensembldb 2.2.0
Epi 2.28
epitools 0.5-10
estimability 1.2
etm 0.6-2
etrunct 0.1
evaluate 0.10.1
exactRankTests 0.8-29
expm 0.999-2
expsmooth 2.3
FactoMineR 1.39
fastcluster 1.1.24
fastICA 1.2-1
fastmatch 1.1-0
FDb.InfiniumMethylation.hg19 2.2.0
fdrtool 1.2.15
FEM 3.6.0
fit.models 0.5-14
flashClust 1.01-2
flexmix 2.3-14
FlowSorted.Blood.450k 1.16.0
FNN 1.1
foreach 1.4.4
forecast 8.2
formattable 0.2.0.1
Formula 1.2-2
fpc 2.1-11
fracdiff 1.4-2
fts 0.9.9
futile.logger 1.4.3
futile.options 1.0.0
gam 1.14-4
gapminder 0.3.0
gclus 1.3.1
gdata 2.18.0
gdsfmt 1.14.1
gdtools 0.1.6
gee 4.13-19
geiger 2.0.6
GenABEL 1.8-0
GenABEL.data 1.0.0
genefilter 1.60.0
geneLenDataBase 1.14.0
GeneOverlap 1.14.0
geneplotter 1.56.0
genetics 1.3.8.1
GenomeInfoDb 1.14.0
GenomeInfoDbData 1.0.0
GenomicAlignments 1.14.1
GenomicFeatures 1.30.0
GenomicFiles 1.14.0
GenomicRanges 1.30.1
GEOquery 2.46.15
getopt 1.20.1
GGally 1.3.2
ggbeeswarm 0.6.0
ggplot2 2.2.1
ggplot2movies 0.0.1
ggpubr 0.1.6
ggrepel 0.7.0
ggsci 2.8
ggsignif 0.4.0
ggtree 1.10.2
git2r 0.21.0
Glimma 1.6.0
glmnet 2.0-13
GlobalOptions 0.0.12
glue 1.2.0
gmailr 0.7.1
gmodels 2.16.2
GO.db 3.5.0
googleVis 0.6.2
goseq 1.30.0
GOstats 2.44.0
gower 0.1.2
gplots 3.0.1
graph 1.56.0
gridBase 0.4-7
gridExtra 2.3
grImport 0.9-0
gsalib 2.1
GSEABase 1.40.1
gsl 1.9-10.3
gtable 0.2.0
gtools 3.5.0
Gviz 1.22.2
haplo.stats 1.7.7
HDF5Array 1.6.0
heatmap3 1.1.1
heatmaply 0.14.0
hexbin 1.27.2
hflights 0.1
hglm 2.1-1
hglm.data 1.0-0
hgu95av2.db 3.2.3
hierfstat 0.04-22
highr 0.6
Hmisc 4.1-1
hms 0.4.0
hom.Hs.inp.db 3.1.2
HSMMSingleCell 0.112.0
htmlTable 1.11.2
htmltools 0.3.6
htmlwidgets 1.0
htSeqTools 1.26.0
httpcode 0.2.0
httpuv 1.3.5
httr 1.3.1
hunspell 2.9
hwriter 1.3.2
ibdreg 0.2.5
idr 1.2
igraph 1.1.2
igraph0 0.5.7
igraphdata 1.0.1
IHW 1.6.0
Illumina450ProbeVariants.db 1.14.0
IlluminaHumanMethylation450kanno.ilmn12.hg19 0.6.0
IlluminaHumanMethylation450kmanifest 0.4.0
IlluminaHumanMethylationEPICanno.ilm10b2.hg19 0.6.0
IlluminaHumanMethylationEPICmanifest 0.3.0
illuminaio 0.20.0
impute 1.52.0
inline 0.3.14
interactiveDisplayBase 1.16.0
ipred 0.9-6
IRanges 2.12.0
IRdisplay 0.4.4
irlba 2.3.2
isva 1.9
iterators 1.0.9
itertools 0.1-3
JADE 2.0-1
jose 0.1
jpeg 0.1-8
jsonlite 1.5
kableExtra 0.7.0
KEGG.db 3.2.3
kernlab 0.9-25
km.ci 0.5-2
KMsurv 0.1-5
knitr 1.18
labeling 0.3
laeken 0.4.6
Lahman 6.0-0
lambda.r 1.2
latticeExtra 0.6-28
lava 1.6
lazyeval 0.2.1
leaps 3.0
LearnBayes 2.15
limma 3.34.5
limSolve 1.5.5.3
lintr 1.0.2
lme4 1.1-15
lmerTest 2.0-36
lmtest 0.9-35
locfit 1.5-9.1
loo 1.1.0
lpSolve 5.6.13
lpsymphony 1.7.1
lsmeans 2.27-61
lubridate 1.7.1
lumi 2.30.0
lumiBarnes 1.18.0
lumiHumanAll.db 1.22.0
lumiHumanIDMapping 1.10.1
MAd 0.8-2
magick 1.8
magrittr 1.5
manhattanly 0.2.0
mapdata 2.2-6
mapproj 1.2-5
maps 3.2.0
maptools 0.9-2
markdown 0.8
marray 1.56.0
MatrixModels 0.4-1
matrixStats 0.52.2
maxLik 1.3-4
maxstat 0.7-25
mclust 5.4
memoise 1.1.0
memuse 4.0-0
MetABEL 0.2-0
metafor 2.0-0
metagenomeSeq 1.20.1
metap 0.9
methylumi 2.24.1
mice 2.46.0
microbenchmark 1.4-3
mime 0.5
minfi 1.24.0
minfiData 0.24.0
minfiDataEPIC 1.4.0
miniUI 0.1.1
minqa 1.2.4
miscTools 0.6-22
missMDA 1.11
missMethyl 1.12.0
mixOmics 6.3.1
mnormt 1.5-5
MODA 1.4.0
ModelMetrics 1.1.0
modeltools 0.2-21
mondate 0.10.01.02
monocle 2.6.1
motifStack 1.22.2
MotIV 1.34.0
multcomp 1.4-8
MultiAssayExperiment 1.4.9
multtest 2.34.0
munsell 0.4.3
mvoutlier 2.0.8
mvtnorm 1.0-6
nanotime 0.2.0
natserv 0.1.4
naturalsort 0.1.3
ncbit 2013.03.29
nleqslv 3.3.1
nloptr 1.0.4
NMF 0.20.6
nor1mix 1.2-3
Nozzle.R1 1.1-1
numDeriv 2016.8-1
nycflights13 0.2.2
openssl 0.9.9
optparse 1.4.4
org.At.tair.db 3.5.0
org.Ce.eg.db 3.5.0
org.Hs.eg.db 3.5.0
org.Mm.eg.db 3.5.0
org.Sc.sgd.db 3.5.0
OrganismDbi 1.20.0
OxyBS 1.5
packrat 0.4.8-1
pamr 1.55
parathyroidSE 1.16.0
pasilla 1.6.0
pbapply 1.3-4
pbkrtest 0.4-7
PBSmodelling 2.68.6
pca3d 0.10
pcaPP 1.9-73
pdftools 1.5
pegas 0.10
permute 0.9-4
phangorn 2.3.1
pheatmap 1.0.8
phylobase 0.8.4
phyloseq 1.22.3
picante 1.6-2
pillar 1.1.0
pinfsc50 1.1.0
pinp 0.0.4
pixmap 0.4-11
pkgconfig 2.0.1
pkgKitten 0.1.4
pkgmaker 0.22
PKI 0.1-5.1
plm 1.6-6
plogr 0.1-1
plotly 4.7.1
plotrix 3.7
plotwidgets 0.4
pls 2.6-0
plyr 1.8.4
png 0.1-7
polspline 1.1.12
poppr 2.6.1
prabclus 2.2-6
pracma 2.1.1
praise 1.0.0
PredictABEL 1.2-2
preprocessCore 1.40.0
prettydoc 0.2.1
prettyunits 1.0.2
processx 2.0.0.1
prodlim 1.6.1
profdpm 3.3
profileModel 0.5-9
progress 1.1.2
ProtGenerics 1.10.0
proto 1.0.0
proxy 0.4-21
pscl 1.5.2
psych 1.7.8
purrr 0.2.4
pvclust 2.0-0
qap 0.1-1
qlcMatrix 0.9.5
qqman 0.1.4
quadprog 1.5-5
quantmod 0.4-12
quantreg 5.34
qvalue 2.10.0
R.cache 0.13.0
R.methodsS3 1.7.1
R.oo 1.21.0
R.rsp 0.42.0
R.utils 2.6.0
R6 2.2.2
RaggedExperiment 1.2.5
randomForest 4.6-12
RANN 2.5.1
rappdirs 0.3.1
rARPACK 0.11-0
raster 2.6-7
rbenchmark 1.0.0
RBGL 1.54.0
RCircos 1.2.0
RColorBrewer 1.1-2
Rcpp 0.12.15
RcppArmadillo 0.8.300.1.0
RcppCCTZ 0.2.3
RcppEigen 0.3.3.3.1
RcppGSL 0.3.3
RcppParallel 4.3.20
RcppRoll 0.2.2
RCurl 1.95-4.10
reactome.db 1.62.0
readr 1.1.1
recipes 0.1.2
regioneR 1.10.0
registry 0.5
rentrez 1.1.0
repr 0.12.0
reshape 0.8.7
reshape2 1.4.3
rex 1.1.2
rGADEM 2.26.0
rgdal 1.2-18
rgl 0.99.9
Rgraphviz 2.22.0
rhdf5 2.22.0
Rhdf5lib 1.0.0
Rhtslib 1.10.0
ritis 0.7.0
rjson 0.2.15
RJSONIO 1.3-0
rlang 0.1.6
rmarkdown 1.8
rms 5.1-2
RMySQL 0.10.14
rncl 0.8.2
RNeXML 2.0.8
rngtools 1.2.4
robCompositions 2.0.6
robust 0.4-18
robustbase 0.92-8
ROC 1.54.0
ROCR 1.0-7
rotl 3.0.3
roxygen2 6.0.1
RPMM 1.25
RPostgreSQL 0.6-2
rprojroot 1.3-2
rrcov 1.4-3
rredlist 0.4.0
Rsamtools 1.30.0
rsconnect 0.8.5
RSpectra 0.12-0
RSQLite 2.0
rstan 2.17.3
rstantools 1.4.0
rstudioapi 0.7
rsvg 1.1
RTCGAToolbox 2.8.0
rticles 0.4.1
rtracklayer 1.38.2
Rtsne 0.13
RUnit 0.4.31
ruv 0.9.7
rvcheck 0.0.9
rversions 1.0.3
rvest 0.3.2
S4Vectors 0.16.0
samr 2.0
sandwich 2.4-0
scales 0.5.0
scater 1.6.2
scatterplot3d 0.3-40
scran 1.6.6
segmented 0.5-3.0
selectr 0.3-1
sendmailR 1.2-1
seqinr 3.4-5
seqLogo 1.44.0
seriation 1.2-2
sfsmisc 1.1-1
sgeostat 1.0-27
shape 1.4.3
shiny 1.0.5
shinydashboard 0.6.1
shinyjs 1.0
shinythemes 1.1.1
ShortRead 1.36.0
showtext 0.5-1
showtextdb 2.0
siggenes 1.52.0
SingleCellExperiment 1.0.0
slam 0.1-42
smoother 1.1
snow 0.4-2
SNPRelate 1.12.2
solrium 1.0.0
sourcetools 0.1.6
sp 1.2-7
spam 2.1-2
SparseM 1.77
spData 0.2.6.9
spdep 0.7-4
spelling 1.1
sphet 1.6
splancs 2.01-40
splm 1.4-10
SQUAREM 2017.10-1
sROC 0.1-2
StanHeaders 2.17.2
statmod 1.4.30
stringdist 0.9.4.6
stringi 1.1.6
stringr 1.2.0
strucchange 1.5-1
subplex 1.4-1
SummarizedExperiment 1.8.1
survey 3.33
survminer 0.4.1
survMisc 0.5.4
sva 3.26.0
svglite 1.2.1
sysfonts 0.7.2
systemPipeR 1.12.0
tagcloud 0.6
taxize 0.9.0
TCC 1.18.0
testthat 2.0.0
TH.data 1.0-8
threejs 0.3.1
tibble 1.4.2
tidyr 0.7.2
tidyselect 0.2.3
tiff 0.1-5
timeDate 3042.101
timeSeries 3042.102
tis 1.34
tkrplot 0.0-23
tmod 0.31
trackViewer 1.14.0
treeio 1.2.1
triebeard 0.3.0
trimcluster 0.1-2
tripack 1.3-8
truncnorm 1.0-7
tseries 0.10-42
TSP 1.1-5
TTR 0.23-2
tufte 0.2
tweeDEseqCountData 1.16.0
TxDb.Celegans.UCSC.ce6.ensGene 3.2.2
TxDb.Dmelanogaster.UCSC.dm3.ensGene 3.2.2
TxDb.Hsapiens.UCSC.hg18.knownGene 3.2.2
TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
TxDb.Hsapiens.UCSC.hg38.knownGene 3.4.0
TxDb.Mmusculus.UCSC.mm10.knownGene 3.4.0
TxDb.Mmusculus.UCSC.mm9.knownGene 3.2.2
TxDb.Rnorvegicus.UCSC.rn4.ensGene 3.2.2
tximport 1.6.0
tximportData 1.6.0
ucminf 1.1-4
UpSetR 1.3.3
urltools 1.7.0
utf8 1.1.3
uuid 0.1-2
VariantAnnotation 1.24.5
vcd 1.4-4
vcfR 1.6.0
vegan 2.4-5
VennDiagram 1.6.18
VGAM 1.0-4
VIM 4.7.0
vipor 0.4.5
viridis 0.4.1
viridisLite 0.2.0
vsn 3.46.0
wateRmelon 1.22.1
waveslim 1.7.5
webp 0.4
webshot 0.5.0
webutils 0.6
WGCNA 1.61
whisker 0.3-2
WikidataR 1.4.0
WikipediR 1.5.0
wikitaxa 0.2.0
withr 2.1.1
worrms 0.2.0
XML 3.98-1.9
xml2 1.1.1
xtable 1.8-2
xts 0.10-1
XVector 0.18.0
yaml 2.1.16
zebrafishRNASeq 0.112.0
zipcode 1.0
zlibbioc 1.24.0
zoo 1.8-1

R_packages/3.4.0

The following R packages are available as part of the R_packages/3.4.0 module, which requires and loads the R/3.4.0 module.  When the R_packages/3.4.0 module is loaded, it adds a directory to the R_LIBS_SITE environment variable.  Within R, these packages will be available via library(package-name).

Package Version
AMOUNTAIN 1.2.0
ASCAT 2.4.4
AnnotationDbi 1.38.2
AnnotationFilter 1.0.0
AnnotationForge 1.18.2
AnnotationHub 2.8.3
BBmisc 1.11
BH 1.65.0-1
BSgenome 1.44.2
BatchJobs 1.6
BiasedUrn 1.07
Biobase 2.36.2
BiocGenerics 0.22.1
BiocInstaller 1.26.1
BiocParallel 1.10.1
Biostrings 2.44.2
Category 2.42.1
ChIPQC 1.12.3
ChIPpeakAnno 3.10.2
DBI 0.7
DESeq 1.28.0
DESeq2 1.16.1
DEXSeq 1.22.0
DEoptimR 1.0-8
DT 0.2
DelayedArray 0.2.7
DiffBind 2.4.8
EMT 1.1
FNN 1.1
Formula 1.2-2
GO.db 3.4.1
GOstats 2.42.0
GSEABase 1.38.2
GenomeInfoDb 1.12.3
GenomeInfoDbData 0.99.0
GenomicAlignments 1.12.2
GenomicFeatures 1.28.5
GenomicRanges 1.28.6
Glimma 1.4.0
Gviz 1.20.0
Hmisc 4.0-3
IRanges 2.10.5
Lahman 6.0-0
LearnBayes 2.15
MODA 1.2.0
MultiAssayExperiment 1.2.1
NMF 0.20.6
Nozzle.R1 1.1-1
ProtGenerics 1.8.0
R6 2.2.2
RBGL 1.52.0
RColorBrewer 1.1-2
RCurl 1.95-4.8
RJSONIO 1.3-0
ROC 1.52.0
RSQLite 2.0
RSpectra 0.12-0
Rcpp 0.12.13
RcppArmadillo 0.8.100.1.0
RcppEigen 0.3.3.3.0
RcppParallel 4.3.20
Rhtslib 1.8.0
Rsamtools 1.28.0
S4Vectors 0.14.7
ShortRead 1.34.2
StanHeaders 2.16.0-1
SummarizedExperiment 1.6.5
TCC 1.16.0
TxDb.Celegans.UCSC.ce6.ensGene 3.2.2
TxDb.Dmelanogaster.UCSC.dm3.ensGene 3.2.2
TxDb.Hsapiens.UCSC.hg18.knownGene 3.2.2
TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
TxDb.Hsapiens.UCSC.hg38.knownGene 3.4.0
TxDb.Mmusculus.UCSC.mm10.knownGene 3.4.0
TxDb.Mmusculus.UCSC.mm9.knownGene 3.2.2
TxDb.Rnorvegicus.UCSC.rn4.ensGene 3.2.2
UpSetR 1.3.3
VariantAnnotation 1.22.3
VennDiagram 1.6.17
WGCNA 1.61
XML 3.98-1.9
XVector 0.16.0
abind 1.4-5
acepack 1.4.1
ade4 1.7-8
adegenet 2.1.0
akima 0.6-2
amap 0.8-14
annotate 1.54.0
ape 4.1
assertthat 0.2.0
backports 1.1.1
base64enc 0.1-3
baySeq 2.10.0
beeswarm 0.2.3
bindr 0.1
bindrcpp 0.2
biomaRt 2.32.1
biomformat 1.4.0
biovizBase 1.24.0
bit 1.1-12
bit64 0.9-7
bitops 1.0-6
blob 1.1.0
brew 1.0-6
caTools 1.17.1
checkmate 1.8.5
chipseq 1.26.1
chron 2.3-51
coda 0.19-1
colorspace 1.3-2
combinat 0.0-8
corpcor 1.6.9
crayon 1.3.4
csaw 1.10.0
curl 3.0
dada2 1.4.0
data.table 1.10.4-3
deSolve 1.20
deldir 0.1-14
dendextend 1.5.2
dichromat 2.0-0
digest 0.6.12
diptest 0.75-7
doParallel 1.0.11
dplyr 0.7.4
dynamicTreeCut 1.63-1
ecodist 2.0.1
edgeR 3.18.1
ellipse 0.3-8
ensembldb 2.0.4
evaluate 0.10.1
expm 0.999-2
fail 1.3
fastcluster 1.1.24
filehash 2.4-1
fit.models 0.5-14
flexmix 2.3-14
foreach 1.4.3
formatR 1.5
fpc 2.1-10
futile.logger 1.4.3
futile.options 1.0.0
gdata 2.18.0
gee 4.13-19
geiger 2.0.6
geneLenDataBase 1.12.0
genefilter 1.58.1
geneplotter 1.54.0
getopt 1.20.0
ggbeeswarm 0.6.0
ggplot2 2.2.1
ggrepel 0.7.0
ggtree 1.8.2
glue 1.2.0
gmodels 2.16.2
goseq 1.28.0
gplots 3.0.1
graph 1.54.0
gridBase 0.4-7
gridExtra 2.3
gtable 0.2.0
gtools 3.5.0
hexbin 1.27.1
hflights 0.1
highr 0.6
htSeqTools 1.24.0
htmlTable 1.9
htmltools 0.3.6
htmlwidgets 0.9
httpuv 1.3.5
httr 1.3.1
hwriter 1.3.2
idr 1.2
igraph 1.1.2
igraph0 0.5.7
impute 1.50.1
inline 0.3.14
interactiveDisplayBase 1.14.0
irlba 2.3.1
iterators 1.0.8
jpeg 0.1-8
jsonlite 1.5
kernlab 0.9-25
knitr 1.17
labeling 0.3
lambda.r 1.2
latticeExtra 0.6-28
lazyeval 0.2.1
limma 3.32.10
lme4 1.1-14
lmerTest 2.0-33
locfit 1.5-9.1
magrittr 1.5
maps 3.2.0
markdown 0.8
matrixStats 0.52.2
mclust 5.3
memoise 1.1.0
memuse 3.0-1
microbenchmark 1.4-2.1
mime 0.5
minqa 1.2.4
mixOmics 6.3.0
modeltools 0.2-21
multtest 2.32.0
munsell 0.4.3
mvtnorm 1.0-6
naturalsort 0.1.3
ncbit 2013.03.29
nloptr 1.0.4
openssl 0.9.7
optparse 1.4.4
org.Mm.eg.db 3.4.1
pca3d 0.10
pcaPP 1.9-72
permute 0.9-4
pheatmap 1.0.8
phyloseq 1.20.0
picante 1.6-2
pinfsc50 1.1.0
pkgconfig 2.0.1
pkgmaker 0.22
plogr 0.1-1
plotrix 3.6-6
plotwidgets 0.4
plyr 1.8.4
png 0.1-7
prabclus 2.2-6
praise 1.0.0
preprocessCore 1.38.1
proto 1.0.0
purrr 0.2.4
pvclust 2.0-0
rARPACK 0.11-0
reactome.db 1.59.1
regioneR 1.8.1
registry 0.3
reshape 0.8.7
reshape2 1.4.2
rgl 0.98.1
rhdf5 2.20.0
rjson 0.2.15
rlang 0.1.2
rmarkdown 1.6
rngtools 1.2.4
robust 0.4-18
robustbase 0.92-7
rprojroot 1.2
rrcov 1.4-3
rtracklayer 1.36.6
rvcheck 0.0.9
samr 2.0
scales 0.5.0
scater 1.4.0
scran 1.4.5
segmented 0.5-2.2
sendmailR 1.2-1
seqinr 3.4-5
shiny 1.0.5
shinydashboard 0.6.1
snow 0.4-2
snpStats 1.26.0
sourcetools 0.1.6
sp 1.2-5
spdep 0.6-15
statmod 1.4.30
stringi 1.1.5
stringr 1.2.0
subplex 1.4-1
sva 3.24.4
systemPipeR 1.10.2
tagcloud 0.6
testit 0.7
testthat 1.0.2
tibble 1.3.4
tidyr 0.7.2
tidyselect 0.2.2
tikzDevice 0.10-1
tkrplot 0.0-23
tmod 0.31
treeio 1.0.2
trimcluster 0.1-2
tximport 1.4.0
vcfR 1.5.0
vegan 2.4-4
vipor 0.4.5
viridis 0.4.0
viridisLite 0.2.0
webshot 0.4.2
whisker 0.3-2
xtable 1.8-2
yaml 2.1.14
zlibbioc 1.22.0
zoo 1.8-0

R_packages/3.3.2

The following R packages are available as part of the R_packages/3.3.2 module, which requires and loads the R/3.3.2 module.  When the R_packages/3.3.2 module is loaded, it adds a directory to the R_LIBS_SITE environment variable.  Within R, these packages will be available via library(package-name).

Package Version
ASCAT 2.4.3
AnnotationDbi 1.36.2
AnnotationHub 2.6.5
BH 1.62.0-1
BSgenome 1.42.0
BiasedUrn 1.07
Biobase 2.34.0
BiocGenerics 0.20.0
BiocInstaller 1.24.0
BiocParallel 1.8.2
Biostrings 2.42.1
DBI 0.6-1
DESeq 1.26.0
DESeq2 1.14.1
DEXSeq 1.20.2
DEoptimR 1.0-8
Formula 1.2-1
GO.db 3.4.0
GenomeInfoDb 1.10.3
GenomicAlignments 1.10.1
GenomicFeatures 1.26.4
GenomicRanges 1.26.4
Gviz 1.18.2
Hmisc 4.0-2
IRanges 2.8.2
LearnBayes 2.15
MODA 1.0.0
NMF 0.20.6
R6 2.2.0
RColorBrewer 1.1-2
RCurl 1.95-4.8
RSQLite 1.1-2
Rcpp 0.12.10
RcppArmadillo 0.7.800.2.0
RcppEigen 0.3.2.9.1
RcppParallel 4.3.20
Rsamtools 1.26.2
S4Vectors 0.12.2
ShortRead 1.32.1
SummarizedExperiment 1.4.0
VariantAnnotation 1.20.3
VennDiagram 1.6.17
WGCNA 1.51
XML 3.98-1.6
XVector 0.14.1
acepack 1.4.1
ade4 1.7-6
adegenet 2.0.1
akima 0.6-2
annotate 1.52.1
ape 4.1
assertthat 0.2.0
backports 1.0.5
base64enc 0.1-3
beeswarm 0.2.3
biomaRt 2.30.0
biovizBase 1.22.0
bitops 1.0-6
caTools 1.17.1
checkmate 1.8.2
chron 2.3-50
coda 0.19-1
colorspace 1.3-2
combinat 0.0-8
crayon 1.3.2
curl 2.5
dada2 1.2.2
data.table 1.10.4
deSolve 1.14
deldir 0.1-14
dendextend 1.5.2
dendextendRcpp 0.6.1
dichromat 2.0-0
digest 0.6.12
diptest 0.75-7
doParallel 1.0.10
dplyr 0.5.0
dynamicTreeCut 1.63-1
edgeR 3.16.5
ellipse 0.3-8
ensembldb 1.6.2
evaluate 0.10
expm 0.999-2
fastcluster 1.1.22
flexmix 2.3-13
foreach 1.4.3
fpc 2.1-10
futile.logger 1.4.3
futile.options 1.0.0
gdata 2.17.0
geiger 2.0.6
geneLenDataBase 1.10.0
genefilter 1.56.0
geneplotter 1.52.0
getopt 1.20.0
ggplot2 2.2.1
ggtree 1.6.11
gmodels 2.16.2
goseq 1.26.0
gplots 3.0.1
gridBase 0.4-7
gridExtra 2.2.1
gtable 0.2.0
gtools 3.5.0
hash 2.2.6
hexbin 1.27.1
highr 0.6
htmlTable 1.9
htmltools 0.3.5
htmlwidgets 0.8
httpuv 1.3.3
httr 1.2.1
hwriter 1.3.2
igraph 1.0.1
impute 1.48.0
interactiveDisplayBase 1.12.0
irlba 2.1.2
iterators 1.0.8
jsonlite 1.4
kernlab 0.9-25
knitr 1.15.1
labeling 0.3
lambda.r 1.1.9
latticeExtra 0.6-28
lazyeval 0.2.0
limma 3.30.13
lme4 1.1-13
lmerTest 2.0-33
locfit 1.5-9.1
magrittr 1.5
maps 3.1.1
markdown 0.8
matrixStats 0.52.2
mclust 5.2.3
memoise 1.1.0
microbenchmark 1.4-2.1
mime 0.5
minqa 1.2.4
modeltools 0.2-21
munsell 0.4.3
mvtnorm 1.0-6
naturalsort 0.1.3
ncbit 2013.03.29
nloptr 1.0.4
openssl 0.9.6
org.Mm.eg.db 3.4.0
pca3d 0.10
permute 0.9-4
picante 1.6-2
pkgmaker 0.22
plogr 0.1-1
plotrix 3.6-4
plotwidgets 0.4
plyr 1.8.4
prabclus 2.2-6
praise 1.0.0
preprocessCore 1.36.0
pvclust 2.0-0
reactome.db 1.58.0
registry 0.3
reshape2 1.4.2
rgl 0.98.1
rmarkdown 1.4
rngtools 1.2.4
robustbase 0.92-7
rprojroot 1.2
rtracklayer 1.34.2
scales 0.4.1
segmented 0.5-1.4
seqinr 3.3-6
shiny 1.0.2
snow 0.4-2
sourcetools 0.1.6
sp 1.2-4
spdep 0.6-13
statmod 1.4.29
stringi 1.1.5
stringr 1.2.0
subplex 1.2-2
sva 3.22.0
tagcloud 0.6
testthat 1.0.2
tibble 1.3.0
tidyr 0.6.1
tkrplot 0.0-23
tmod 0.31
trimcluster 0.1-2
vegan 2.4-3
viridis 0.4.0
viridisLite 0.2.0
whisker 0.3-2
xtable 1.8-2
yaml 2.1.14
zlibbioc 1.20.0
zoo 1.8-0

R_packages/3.3.1

The following R packages are available as part of the R_packages/3.3.1 module, which requires and loads the R/3.3.1 module.  When the R_packages/3.3.1 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these should be available via library(package-name).

Package Version
ASCAT 2.4.3
AnnotationDbi 1.36.0
AnnotationHub 2.6.0
BH 1.60.0-2
BSgenome 1.42.0
BiasedUrn 1.07
Biobase 2.34.0
BiocGenerics 0.20.0
BiocInstaller 1.24.0
BiocParallel 1.8.0
Biostrings 2.42.0
DBI 0.5-1
DESeq 1.26.0
DESeq2 1.14.0
DEXSeq 1.20.0
DEoptimR 1.0-6
Formula 1.2-1
GO.db 3.4.0
GenomeInfoDb 1.10.0
GenomicAlignments 1.10.0
GenomicFeatures 1.26.0
GenomicRanges 1.26.1
Gviz 1.18.0
Hmisc 3.17-4
IRanges 2.8.0
LearnBayes 2.15
NMF 0.20.6
R6 2.2.0
RColorBrewer 1.1-2
RCurl 1.95-4.8
RSQLite 1.0.0
Rcpp 0.12.7
RcppArmadillo 0.7.500.0.0
RcppEigen 0.3.2.9.0
RcppParallel 4.3.20
Rsamtools 1.26.1
S4Vectors 0.12.0
ShortRead 1.32.0
SummarizedExperiment 1.4.0
VariantAnnotation 1.20.0
VennDiagram 1.6.17
XML 3.98-1.4
XVector 0.14.0
acepack 1.4.0
ade4 1.7-4
adegenet 2.0.1
akima 0.5-12
annotate 1.52.0
ape 3.5
assertthat 0.1
base64enc 0.1-3
beeswarm 0.2.3
biomaRt 2.30.0
biovizBase 1.22.0
bitops 1.0-6
caTools 1.17.1
chron 2.3-47
coda 0.18-1
colorspace 1.2-7
combinat 0.0-8
crayon 1.3.2
curl 2.2
dada2 1.2.0
data.table 1.9.6
deSolve 1.14
deldir 0.1-12
dendextend 1.3.0
dendextendRcpp 0.6.1
dichromat 2.0-0
digest 0.6.10
diptest 0.75-7
doParallel 1.0.10
dplyr 0.5.0
edgeR 3.16.0
ellipse 0.3-8
ensembldb 1.6.0
evaluate 0.10
flexmix 2.3-13
foreach 1.4.3
formatR 1.4
fpc 2.1-10
futile.logger 1.4.3
futile.options 1.0.0
gdata 2.17.0
geiger 2.0.6
geneLenDataBase 1.10.0
genefilter 1.56.0
geneplotter 1.52.0
getopt 1.20.0
ggplot2 2.1.0
ggtree 1.6.0
gmodels 2.16.2
goseq 1.26.0
gplots 3.0.1
gridBase 0.4-7
gridExtra 2.2.1
gtable 0.2.0
gtools 3.5.0
hexbin 1.27.1
highr 0.6
htmltools 0.3.5
htmlwidgets 0.8
httpuv 1.3.3
httr 1.2.1
hwriter 1.3.2
igraph 1.0.1
interactiveDisplayBase 1.12.0
irlba 2.1.2
iterators 1.0.8
jsonlite 1.1
kernlab 0.9-25
knitr 1.14
labeling 0.3
lambda.r 1.1.9
latticeExtra 0.6-28
lazyeval 0.2.0
limma 3.30.0
lme4 1.1-12
lmerTest 2.0-32
locfit 1.5-9.1
magrittr 1.5
maps 3.1.1
markdown 0.7.7
matrixStats 0.51.0
mclust 5.2
microbenchmark 1.4-2.1
mime 0.5
minqa 1.2.4
modeltools 0.2-21
munsell 0.4.3
mvtnorm 1.0-5
naturalsort 0.1.3
ncbit 2013.03.29
nloptr 1.0.4
openssl 0.9.4
org.Mm.eg.db 3.4.0
pca3d 0.10
permute 0.9-4
picante 1.6-2
pkgmaker 0.22
plotrix 3.6-3
plotwidgets 0.4
plyr 1.8.4
prabclus 2.2-6
praise 1.0.0
pvclust 2.0-0
reactome.db 1.55.0
registry 0.3
reshape2 1.4.2
rgl 0.98.1
rmarkdown 1.1
rngtools 1.2.4
robustbase 0.92-6
rtracklayer 1.34.0
scales 0.4.0
segmented 0.5-1.4
seqinr 3.3-3
shiny 0.14.1
snow 0.4-2
sourcetools 0.1.5
sp 1.2-3
spdep 0.6-8
statmod 1.4.26
stringi 1.1.2
stringr 1.1.0
subplex 1.1-6
sva 3.22.0
tagcloud 0.6
testthat 1.0.2
tibble 1.2
tidyr 0.6.0
tkrplot 0.0-23
tmod 0.31
trimcluster 0.1-2
vegan 2.4-1
whisker 0.3-2
xtable 1.8-2
yaml 2.1.13
zlibbioc 1.20.0
zoo 1.7-13

R_packages/3.3.0

The following R packages are available as part of the R_packages/3.3.0 module, which requires and loads the R/3.3.0 module.  When the R_packages/3.3.0 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these should be available via library(package-name).

Package Version
AnnotationDbi 1.34.4
AnnotationHub 2.4.2
BH 1.60.0-2
BSgenome 1.40.1
BiasedUrn 1.07
Biobase 2.32.0
BiocGenerics 0.18.0
BiocInstaller 1.22.3
BiocParallel 1.6.6
Biostrings 2.40.2
DBI 0.5-1
DESeq 1.24.0
DESeq2 1.12.4
DEXSeq 1.18.4
DEoptimR 1.0-6
Formula 1.2-1
GO.db 3.3.0
GenomeInfoDb 1.8.7
GenomicAlignments 1.8.4
GenomicFeatures 1.24.5
GenomicRanges 1.24.3
Gviz 1.16.5
Hmisc 3.17-4
IRanges 2.6.1
LearnBayes 2.15
NMF 0.20.6
R6 2.2.0
RColorBrewer 1.1-2
RCurl 1.95-4.8
RSQLite 1.0.0
Rcpp 0.12.7
RcppArmadillo 0.7.400.2.0
RcppEigen 0.3.2.9.0
Rhtslib 1.4.3
Rsamtools 1.24.0
S4Vectors 0.10.3
ShortRead 1.30.0
SummarizedExperiment 1.2.3
VariantAnnotation 1.18.7
VennDiagram 1.6.17
XML 3.98-1.4
XVector 0.12.1
acepack 1.3-3.3
ade4 1.7-4
adegenet 2.0.1
akima 0.5-12
annotate 1.50.1
ape 3.5
assertthat 0.1
base64enc 0.1-3
beeswarm 0.2.3
biomaRt 2.28.0
biovizBase 1.20.0
bitops 1.0-6
caTools 1.17.1
chron 2.3-47
coda 0.18-1
colorspace 1.2-7
combinat 0.0-8
crayon 1.3.2
curl 2.1
dada2 1.0.3
data.table 1.9.6
deSolve 1.14
deldir 0.1-12
dendextend 1.3.0
dendextendRcpp 0.6.1
dichromat 2.0-0
digest 0.6.10
diptest 0.75-7
doParallel 1.0.10
dplyr 0.5.0
edgeR 3.14.0
ellipse 0.3-8
ensembldb 1.4.7
evaluate 0.10
fields 8.4-1
flexmix 2.3-13
foreach 1.4.3
formatR 1.4
fpc 2.1-10
futile.logger 1.4.3
futile.options 1.0.0
gdata 2.17.0
geiger 2.0.6
geneLenDataBase 1.8.0
genefilter 1.54.2
geneplotter 1.50.0
getopt 1.20.0
ggplot2 2.1.0
gmodels 2.16.2
goseq 1.24.0
gplots 3.0.1
gridBase 0.4-7
gridExtra 2.2.1
gtable 0.2.0
gtools 3.5.0
hexbin 1.27.1
highr 0.6
htmltools 0.3.5
htmlwidgets 0.8
httpuv 1.3.3
httr 1.2.1
hwriter 1.3.2
igraph 1.0.1
interactiveDisplayBase 1.10.3
irlba 2.1.2
iterators 1.0.8
jsonlite 1.1
kernlab 0.9-25
knitr 1.14
labeling 0.3
lambda.r 1.1.9
latticeExtra 0.6-28
lazyeval 0.2.0
limma 3.28.21
lme4 1.1-12
lmerTest 2.0-32
locfit 1.5-9.1
magrittr 1.5
maps 3.1.1
markdown 0.7.7
matrixStats 0.51.0
mclust 5.2
memoise 1.0.0
microbenchmark 1.4-2.1
mime 0.5
minqa 1.2.4
modeltools 0.2-21
munsell 0.4.3
mvtnorm 1.0-5
naturalsort 0.1.3
ncbit 2013.03.29
nloptr 1.0.4
openssl 0.9.4
org.Mm.eg.db 3.3.0
pca3d 0.10
permute 0.9-4
picante 1.6-2
pkgmaker 0.22
plotrix 3.6-3
plotwidgets 0.4
plyr 1.8.4
prabclus 2.2-6
praise 1.0.0
pvclust 2.0-0
reactome.db 1.55.0
registry 0.3
reshape2 1.4.1
rgl 0.98.1
rmarkdown 1.1
rngtools 1.2.4
robustbase 0.92-6
rtracklayer 1.32.2
scales 0.4.0
segmented 0.5-1.4
seqinr 3.3-3
shiny 0.14.1
snow 0.4-2
sourcetools 0.1.5
sp 1.2-3
spam 1.4-0
spdep 0.6-8
statmod 1.4.26
stringi 1.1.2
stringr 1.1.0
subplex 1.1-6
sva 3.20.0
tagcloud 0.6
testthat 1.0.2
tibble 1.2
tidyr 0.6.0
tkrplot 0.0-23
tmod 0.31
trimcluster 0.1-2
vegan 2.4-1
whisker 0.3-2
xtable 1.8-2
yaml 2.1.13
zlibbioc 1.18.0
zoo 1.7-13