Bioconductor 3.7

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.

The core BlueBEAR Bioconductor bundle includes over 100 libraries – please note that additional Bioconductor packages can be found on the Extra R Libraries page (e.g. GOTHiC). If you need a Bioconductor library that is not included or available then please make a request to the IT Service Desk.

Accessing the software

To load the module:

$ module load R-bundle-Bioconductor/3.7-iomkl-2018a-R-3.5.0

Additional Packages

List of currently installed packages
Package Version
acepack 1.4.1
ade4 1.7-11
affy 1.58.0
affycoretools 1.52.0
affyio 1.50.0
AgiMicroRna 2.30.0
ALDEx2 1.12.0
annaffy 1.52.0
annotate 1.58.0
AnnotationDbi 1.42.1
AnnotationFilter 1.4.0
AnnotationForge 1.22.0
AnnotationHub 2.12.0
ape 5.1
assertthat 0.2.0
backports 1.1.2
ballgown 2.12.0
base64 2.0
base64enc 0.1-3
baySeq 2.14.0
beachmat 1.2.0
beanplot 1.2
beeswarm 0.2.3
bindr 0.1.1
bindrcpp 0.2.2
Biobase 2.40.0
BiocGenerics 0.26.0
BiocInstaller 1.30.0
BiocParallel 1.14.1
biomaRt 2.36.0
biomformat 1.8.0
Biostrings 2.48.0
biovizBase 1.28.0
bit 1.1-12
bit64 0.9-7
bitops 1.0-6
blob 1.1.1
BSgenome 1.48.0
BSgenome.Hsapiens.UCSC.hg19 1.4.0
bumphunter 1.22.0
Category 2.46.0
caTools 1.17.1
CGHbase 1.40.0
checkmate 1.8.5
circlize 0.4.3
class 7.3-14
cli 1.0.0
cluster 2.0.7-1
codetools 0.2-15
colorspace 1.3-2
ComplexHeatmap 1.18.0
corpcor 1.6.9
crayon 1.3.4
crosstalk 1.0.0
cummeRbund 2.22.0
curl 3.2
dada2 1.8.0
data.table 1.11.2
DBI 1.0.0
DEGseq 1.34.0
DelayedArray 0.6.0
DelayedMatrixStats 1.2.0
DEoptimR 1.0-8
derfinder 1.14.0
derfinderHelper 1.14.0
DESeq2 1.20.0
dichromat 2.0-0
digest 0.6.15
DNAcopy 1.54.0
doParallel 1.0.11
doRNG 1.6.6
dplyr 0.7.4
DT 0.4
dupRadar 1.10.0
dynamicTreeCut 1.63-1
DynDoc 1.58.0
e1071 1.6-8
edgeR 3.22.1
ellipse 0.4.1
ensembldb 2.4.1
evaluate 0.10.1
FDb.InfiniumMethylation.hg19 2.2.0
ff 2.2-13
FNN 1.1
foreach 1.4.4
foreign 0.8-70
formatR 1.5
Formula 1.2-3
futile.logger 1.4.3
futile.options 1.0.1
gcrma 2.52.0
gdata 2.18.0
gdsfmt 1.16.0
genefilter 1.62.0
geneLenDataBase 1.16.0
geneplotter 1.58.0
GENIE3 1.2.0
GenomeGraphs 1.40.0
GenomeInfoDb 1.16.0
GenomeInfoDbData 1.1.0
GenomicAlignments 1.16.0
GenomicFeatures 1.32.0
GenomicFiles 1.16.0
GenomicRanges 1.32.2
genoset 1.36.0
GEOquery 2.48.0
GetoptLong 0.1.6
GGally 1.3.2
ggbeeswarm 0.6.0
ggbio 1.28.0
ggplot2 2.2.1
GlobalOptions 0.0.13
glue 1.2.0
GO.db 3.6.0
goseq 1.32.0
GOstats 2.46.0
gplots 3.0.1
graph 1.58.0
gridExtra 2.3
GSEABase 1.42.0
gtable 0.2.0
gtools 3.5.0
Gviz 1.24.0
HCsnip 1.17.0
HDF5Array 1.8.0
hgu133plus2.db 3.2.3
highr 0.6
Hmisc 4.1-1
hms 0.4.2
Homo.sapiens 1.3.1
htmlTable 1.11.2
htmltools 0.3.6
htmlwidgets 1.2
httpuv 1.4.3
httr 1.3.1
hwriter 1.3.2
igraph 1.2.1
illuminaio 0.22.0
impute 1.54.0
interactiveDisplayBase 1.18.0
IRanges 2.14.9
iterators 1.0.9
jsonlite 1.5
KEGG.db 3.2.3
KEGGgraph 1.40.0
KEGGprofile 1.22.0
KEGGREST 1.20.0
KernSmooth 2.23-15
knitr 1.20
labeling 0.3
lambda.r 1.2.2
later 0.7.2
lattice 0.20-35
latticeExtra 0.6-28
lazyeval 0.2.1
LEA 2.2.0
limma 3.36.1
locfit 1.5-9.1
logspline 2.1.9
lumi 2.32.0
magrittr 1.5
manipulateWidget 0.9.0
markdown 0.8
marray 1.58.0
maSigPro 1.52.0
MASS 7.3-50
Matrix 1.2-14
matrixStats 0.53.1
mclust 5.4
memoise 1.1.0
metagenomeSeq 1.22.0
methylumi 2.26.0
Mfuzz 2.40.0
mgcv 1.8-23
mime 0.5
minfi 1.26.0
miniUI 0.1.1
mixOmics 6.3.1
multtest 2.36.0
munsell 0.4.3
mvtnorm 1.0-7
nleqslv 3.3.1
nlme 3.1-137
nnet 7.3-12
NOISeq 2.24.0
nor1mix 1.2-3
oligoClasses 1.42.0
openssl 1.0.1
org.Hs.eg.db 3.6.0
OrganismDbi 1.22.0
pcaMethods 1.72.0
pcaPP 1.9-73
penalized 0.9-50
perm 1.0-0.0
permute 0.9-4
PFAM.db 3.6.0
pheatmap 1.0.8
phyloseq 1.24.0
pillar 1.2.2
pkgconfig 2.0.1
pkgmaker 0.22
plyr 1.8.4
png 0.1-7
polyester 1.16.0
preprocessCore 1.42.0
prettyunits 1.0.2
progress 1.1.2
promises 1.0.1
ProtGenerics 1.12.0
purrr 0.2.4
quadprog 1.5-5
qvalue 2.12.0
R.methodsS3 1.7.1
R.oo 1.22.0
R.utils 2.6.0
R6 2.2.2
rARPACK 0.11-0
RBGL 1.56.0
RColorBrewer 1.1-2
Rcpp 0.12.16
RcppParallel 4.4.0
RCurl 1.95-4.10
readr 1.1.1
registry 0.5
ReportingTools 2.20.0
reshape 0.8.7
reshape2 1.4.3
rgl 0.99.16
Rgraphviz 2.24.0
rhdf5 2.24.0
Rhdf5lib 1.2.0
rjson 0.2.18
rlang 0.2.0
RNASeqPower 1.20.0
rngtools 1.2.4
robustbase 0.93-0
ROCR 1.0-7
rpart 4.1-13
rrcov 1.4-3
Rsamtools 1.32.0
RSpectra 0.12-0
RSQLite 2.1.1
rstudioapi 0.7
Rsubread 1.30.1
rtracklayer 1.40.2
S4Vectors 0.18.1
samr 2.0
SC3 1.8.0
scales 0.5.0
scater 1.8.0
scran 1.8.1
shape 1.4.4
shiny 1.0.5
shinydashboard 0.7.0
ShortRead 1.38.0
sigaR 1.28.0
siggenes 1.54.0
SingleCellExperiment 1.2.0
snow 0.4-2
snowfall 1.84-6.1
SNPRelate 1.14.0
sourcetools 0.1.7
SPIA 2.32.0
statmod 1.4.30
stringi 1.2.2
stringr 1.3.1
SummarizedExperiment 1.10.1
survival 2.42-3
sva 3.28.0
TeachingDemos 2.10
tibble 1.4.2
tidyr 0.8.0
tidyselect 0.2.4
tkWidgets 1.58.0
TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
tximport 1.8.0
utf8 1.1.3
VariantAnnotation 1.26.0
vegan 2.5-1
venn 1.6
vipor 0.4.5
viridis 0.5.1
viridisLite 0.3.0
widgetTools 1.58.0
WriteXLS 4.0.0
XML 3.98-1.11
xml2 1.2.0
xtable 1.8-2
XVector 0.20.0
yaml 2.1.19
zlibbioc 1.26.0

To view installed packages in R, run the following commands with the module loaded:

$ R
> installed.packages()

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by ITServices or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

Known Problems & Limitations

None.

Other Information

The Support Level for this application isAn.

Visit theBioconductor website for more information regarding this application.


Last modified:7 June2018