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R is a free software environment for statistical computing and graphics.

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Seminar Slides

Programming (A. Pacheco, J. Mack)
Visualization (A. Pacheco, J. Mack)

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title	Deprecated CentOS 7.x Software: Use module load cent7 to use the following modules

Which versions of R are available?

There are four version of R available, 3.3.3, 3.4.2, 3.4.3 and 3.5.3. Of the two 3.5.3 version, one version labelled r-bio contains packages from Bioconductor for Bioinformatics research.

Usage

Code Block

language	bash
title	R 3.3.3

module load r-project/3.3.3

Code Block

language	bash
title	R 3.4.2

module load r-project/3.4.2

Code Block

language	bash
title	R 3.4.3

module load anaconda/python3

Code Block

language	bash
title	R 3.5.3

module load r-project/3.5.3

Code Block

language	bash
title	r 3.5.3 for Bioinformatics

module load r-bio/3.5.3

How to install R packages?

A variety of R packages are installed however it is recommended that users install packages (newer and updated versions) in their own home directory.

The r-project/3.x.y modules sets up a variable, R_LIBS, to install packages in your home directory. Make sure the R_LIBS directory exists

Code Block

language	bash

mkdir -p ${R_LIBS}

Start interactive R session and install package using the command

Code Block

language	bash

install.packages('packagename')

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If you get an error installing packages locally, then use the command

Code Block

language	bash

install.packages('packagename',lib=Sys.getenv("R_LIBS"))

Installed Packages

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Package

...

3.3.3

...

3.4.2

...

3.4.3

...

3.5.3

...

abind

...

1.4-5

...

1.4-5

...

askpass

...

1.1

...

1.1

...

1.1

...

assertthat

...

0.2.0

...

0.2.0

...

0.2.0

...

0.2.0

...

backports

...

1.1.2

...

1.1.1

...

1.1.2

...

1.1.3

...

base

...

3.3.3

...

3.4.2

...

3.4.3

...

3.5.3

...

base64enc

...

0.1-3

...

0.1-3

...

0.1-3

...

0.1-3

...

BH

...

1.65.0-1

...

1.65.0-1

...

1.65.0-1

...

1.69.0-1

...

bindr

...

0.1

...

0.1

...

0.1

...

bindrcpp

...

0.2

...

0.2

...

0.2

...

bitops

...

1.0-6

...

1.0-6

...

1.0-6

...

boot

...

1.3-18

...

1.3-20

...

1.3-20

...

1.3-20

...

broom

...

0.4.3

...

0.4.3

...

0.4.3

...

0.5.1

...

callr

...

3.2.0

...

2.0.1

...

1.0.0

...

3.1.1

...

car

...

2.1-6

...

caret

...

6.0-78

...

caTools

...

1.17.1.2

...

1.17.1

...

1.17.1

...

cellranger

...

1.1.0

...

1.1.0

...

1.1.0

...

1.1.0

...

chron

...

2.3-51

...

class

...

7.3-14

...

7.3-14

...

7.3-14

...

7.3-15

...

R is a free software environment for statistical computing and graphics.

Version	module name	build	notes
4.0.3	r/4.0.3	SPACK using gcc 8.3.1	optimized for avx, avx2 and avx512
4.0.5	conda/r	Conda packages	Load anaconda3/2020.07 first
4.1.1	conda/spark	Conda packages	Load anaconda3/2020.07 first. For use with Apache Spark

Seminar Slides

Installed Packages

R packages are built using SPACK optimized for the underlying CPU architecture or binary installs using Conda. Applications built by RC staff that are dependent on R use the SPACK built R packages.

Info
The `conda/spark` module was built for use with Apache Spark and provides Python packages such as pyspark

Expand

title	Package List (as of Dec 10, 2021)

Package	4.0.3 SPACK	4.0.5 Conda	4.1.1 SPARK
abind		1.4-5	1.4-5
acepack	1.4.1
amap	0.8-17
animation	2.6
annotate	1.62.0
AnnotationDbi	1.46.1
ape	5.3
argparse	2.0.1
askpass	1.1	1.1	1.1
assertthat	0.2.1	0.2.1	0.2.1
backports	1.1.4	1.4.0	1.4.0
base	4.0.3	4.0.5	4.1.1
base64enc	0.1-3	0.1-3	0.1-3
BBmisc	1.11
BH	1.69.0-1
BiasedUrn	1.07
bibtex	0.4.2
bigmemory	4.5.36
bigmemory.sri	0.1.3
Biobase	2.44.0
BiocGenerics	0.34.0
BiocManager	1.30.10	1.30.16	1.30.16
BiocParallel	1.18.1
BiocVersion			3.14.0
biomaRt	2.40.5
Biostrings	2.52.0
bit	1.1-14	4.0.4	4.0.4
bit64	0.9-7	4.0.5	4.0.5
bitops	1.0-6	1.0-7	1.0-7
blob	1.2.0	1.2.2	1.2.2
boot	1.3-27	1.3-28	1.3-28
brew	1.0-6
brio		1.1.3	1.1.3
broom	0.5.2	0.7.10	0.7.10
bslib		0.3.1	0.3.1
cachem		1.0.6	1.0.6
callr	3.4.3	3.7.0	3.7.0
car		3.0-12	3.0-12
carData		3.0-4	3.0-4
caret	6.0-84	6.0-90	6.0-90
caTools	1.17.1.2
cellranger	1.1.0	1.1.0	1.1.0
checkmate	1.9.4
chron	2.3-53
class	7.3-18	7.3-19	7.3-19
cli	2.0.2	3.1.0	3.1.0
clipr	0.7.0	0.7.1	0.7.1
cluster	2.1.1	2.1.2	2.1.2
clusterGeneration	1.3.4
coda	0.19-3
codetools	0.2-18	0.2-18	0.2-18
colorspace	1.4-1	2.0-2	2.0-2
combinat	0.0-8
commonmark	1.7	1.7	1.7
compiler	4.0.3	4.0.5	4.1.1
config		0.3.1	0.3.1
conquer		1.2.1	1.2.1
corrplot		0.92	0.92
covr	3.5.0
cowplot	1.0.0	1.1.1	1.1.1
cpp11		0.4.2	0.4.2
crayon	1.3.4	1.4.2	1.4.2
crosstalk	1.0.0	1.2.0	1.2.0
crul		1.2.0	1.2.0
ctc	1.58.0
curl	4.3	4.3.2	4.3.2
data.table	1.12.8	1.14.2	1.14.2
datasets	4.0.3	4.0.5	4.1.1
DBI	1.1.0	1.1.1	1.1.1
dbplyr	1.4.2	2.1.1	2.1.1
DelayedArray	0.10.0
dendextend	1.12.0
desc	1.2.0	1.4.0	1.4.0
DESeq2	1.24.0
devtools	2.3.0
DEXSeq	1.36.0
DiagrammeR		1.0.6.1	1.0.6.1
diffobj		0.3.5	0.3.5
digest	0.6.25	0.6.29	0.6.29
doParallel	1.0.15
downloader		0.4	0.4
dplyr	0.8.3	1.0.7	1.0.7
dqrng	0.2.1
DT	0.13	0.20	0.20
dtplyr		1.2.0	1.2.0
dygraphs	1.1.1.6	1.1.1.6	1.1.1.6
e1071		1.7-9	1.7-9
edgeR	3.26.8
ellipsis	0.3.0	0.3.2	0.3.2
evaluate	0.14	0.14	0.14
expm	0.999-4
fansi	0.4.0	0.5.0	0.4.2
farver		2.1.0	2.1.0
fastcluster	1.1.25
fastmap		1.1.0	1.1.0
fastmatch	1.1-0
findpython	1.0.5
fitdistrplus	1.0-14
flexdashboard		0.5.2	0.5.2
FNN	1.1.3
fontawesome		0.2.2	0.2.2
forcats	0.4.0	0.5.1	0.5.1
foreach	1.4.7	1.5.1	1.5.1
foreign	0.8-81	0.8-81	0.8-81
forge		0.2.0	0.2.0
formatR	1.7	1.11	1.11
Formula	1.2-3
fs	1.3.1	1.5.2	1.5.2
futile.logger	1.4.3
futile.options	1.0.1
future	1.14.0	1.23.0	1.23.0
future.apply	1.3.0	1.8.1	1.8.1
gapminder		0.3.0	0.3.0
gargle		1.2.0	1.2.0
gbRd	0.4-11
gdata	2.18.0
gdtools		0.2.3	0.2.3
genefilter	1.72.1
geneLenDataBase	1.20.0
geneplotter	1.62.0
generics	0.0.2	0.1.1	0.1.1
GenomeInfoDb	1.20.0
GenomeInfoDbData	1.2.1
GenomicAlignments	1.20.1
GenomicFeatures	1.36.4
GenomicRanges	1.36.1
gganimate		1.0.7	1.0.7
ggdendro	0.1-20
ggplot2	3.2.0	3.3.5	3.3.5
ggpubr		0.4.0	0.4.0
ggrepel	0.8.1	0.9.1	0.9.1
ggridges	0.5.1
ggsci		2.9	2.9
ggsignif		0.6.3	0.6.3
ggthemes		4.2.4	4.2.4
ggvis		0.4.7	0.4.7
gh	1.1.0
gistr	0.4.2	0.9.0	0.9.0
git2r	0.27.1
Glimma	1.12.0
glmnet		4.1-2	4.1-2
globals	0.12.4	0.14.0	0.14.0
glue	1.4.1	1.5.1	1.5.1
gmodels	2.18.1
GO.db	3.4.1
googleAuthR			1.4.0
googledrive		2.0.0	2.0.0
googlesheets4		1.0.0	1.0.0
googleVis

1

0.6.10

0.

0

6.10
GOplot	1.0.

1

2
goseq	1.36.0
gower	0.2.1

clipr

0.2.2

0.

4

2.

0

2
gplots	3.0.

5

1.

0

1
graphics	4.0.3	4.

0

0.5

.0

0.

4.

0

clisymbols

1.

2.0

1.2.0

cluster

2

1
grDevices	4.0.3	4.0.5

2

4.

0

1.

6

1

grid

2

4.0.

6

3

2

4.0.

7-1

5

2

4.

0

1.

7-

1

codetools

gridExtra

0.

2

-15

0.2-15

0.2-16

colorspace

1.3-2

1.4-0

1.3-2

compiler

3.3.3

3.4.2

3.4.3

3.5.3

3.5.3covr3.0.1

crayon

1.3.4

1.3.4ctc1.54.0

curl

3.1

3.3

CVST

0.2-1

datasets

3.3.3

3.4.2

3.4.3

3.5.3

data.table

1.10.4-3

1.11.8

DBI

0.7

1.0.0

0.7

dbplyr

1.2.0

1.1.0

1.3.0

1.2.2

ddalpha

1.3.1

debugme

1.1.0

DelayedArray0.6.5

DEoptimR

1.0-8

desc

1.2.0

devtools

2.0.1

1.12.0

dichromat

2.0-0

digest

0.6.14

0.6.12

0.6.13

0.6.18

0.6.12

dimRed

0.1.0

dplyr

0.7.4

0.8.0.1

0.7.7

DRR

0.0.2

dygraphs

1.1.1.6

1.1.1.4

ellipsis

0.1.0

evaluate

0.10.1

0.13

0.10.1

fansi

0.4.0

1.1.25fftwtools0.9-8findpython1.0.3

flexdashboard

0.5.1.1

0.5.1

forcats

0.2.0

0.4.0

0.2.0

foreach

1.4.4

foreign

0.8-67

0.8-69

0.8-71

formatR

1.5

fs

1.2.6

1.2.7

1.2.6

genefilter1.62.0GenomeInfoDb1.16.0GenomeInfoDbData1.1.0GenomicRanges1.32.6

generics

0.0.2

ggplot2

2.2.1

3.1.0

3.2.0

gh

1.0.1

git2r

0.24.0

0.25.2

0.24.0

0.18.0

glmnet

2.0-13

glue

1.2.0

1.3.1

1.2.0

gower

0.1.2

graphics

3.3.3

3.4.2

3.4.3

3.5.3

grDevices

3.3.3

3.4.2

3.4.3

3.5.3

grid

3.3.3

3.4.2

3.4.3

3.5.3

gtable

0.2.0

gtools

3.8.1

3.5.0

haven

1.1.1

1.1.0

2.1.0

1.1.0

hexbin

1.27.1

highr

0.6

0.7

0.6

hms

0.4.0

0.4.1

0.4.0

0.4.2

0.3

htmltools

0.3.6

htmlwidgets

1.3

0.9

httpuv

1.5.1

1.3.5

httr

1.3.1

1.4.0

1.3.1

ini

0.3.1

ipred

0.9-6

IRdisplay

0.4.4

IRkernel

0.8.11

iterators

1.0.9

jsonlite

1.5

1.6

1.5

kernlab

0.9-25

KernSmooth

2.23-15

knitr

1.18

1.19

1.18

1.22

labeling

0.3

later

0.8.0

lattice

0.20-34

0.20-35

0.20-38

lava

1.5.1

lazyeval

0.2.1

0.2.0

0.2.1

0.2.0

lme4

1.1-15

lubridate

1.7.1

1.7.2

1.7.1

1.7.4

1.7.1

magrittr

1.5

maps

3.2.0

markdown

0.8

0.9

0.8

MASS

7.3-45

7.3-47

7.3-48

7.3-51.1

Matrix

1.2-8

1.2-11

1.2-12

1.2-15

MatrixModels

0.4-1

0.52.2

matrixStats

0.54.0

0.53.1

memoise

1.1.0

methods

3.3.3

3.4.2

3.4.3

3.5.3

mgcv

1.8-17

1.8-20

1.8-22

1.8-27

mime

0.5

0.6

0.5

minqa

1.2.4

mnormt

1.5-5

ModelMetrics

1.1.0

modelr

0.1.1

0.1.4

munsell

0.4.3

0.5.0

0.4.3

nlme

3.1-131

3.1-137

nloptr

1.0.4

nnet

7.3-12

numDeriv

2016.8-1

openssl

0.9.9

1.2.2

0.9.7optparse1.6.0

padr

0.4.1

0.4.0

parallel

3.3.3

3.4.2

3.4.3

3.5.3

pbdZMQ

0.3-0

pbkrtest

0.4-7

phangorn2.5.5

pillar

1.1.0

1.0.1

1.3.1

pkgbuild

1.0.2

1.0.3

1.0.2

pkgconfig

2.0.1

2.0.2

pkgload

1.0.2

plogr

0.1-1

0.2.0

0.2.0plot3D1.1.1

plyr

1.8.4

png

0.1-7

pracma

2.2.5

2.1.4

praise

1.0.0

prettyunits

1.0.2

processx

3.3.0

3.2.0

prodlim

1.6.1

progress

1.2.0

1.1.2

promises

1.0.1

proto

1.0.0

ps

1.3.0

1.1.0

psych

1.7.8

purrr

0.2.4

0.3.1

0.2.4

quantmod

0.4-12

quantreg

5.34

R6

2.2.2

2.4.0

2.2.2

randomForest

4.6-12

rbokeh

0.6.3

rcmdcheck

1.3.2

RColorBrewer

1.1-2

Rcpp

0.12.15

0.12.13

0.12.14

1.0.0

1.0.0RcppArmadillo0.8.100.1.0

RcppEigen

0.3.3.3.1

RcppRoll

0.2.2

RCurl1.95-4.8

readr

1.1.1

1.3.1

1.1.1

readxl

1.0.0

1.3.1

1.1.0

recipes

0.1.1

rematch

1.0.1

remotes

2.0.2

2.0.4

2.0.2

repr

0.12.0

reprex

0.1.1

0.1.2

0.1.1

0.2.1

reshape2

1.4.3

1.4.2

1.4.3

1.4.2

RJSONIO

1.3-0

rlang

0.1.6

0.3.1

rmarkdown

1.8

1.6

1.8

1.12

R.matlab

3.6.2

3.6.1

R.methodsS3

1.7.1

Rmpi0.6-6

robustbase

0.92-8

R.oo

1.22.0

1.21.0

rpart

4.1-10

4.1-11

4.1-13

rprojroot

1.3-2

1.2

1.3-1

1.3-2

1.2Rsamtools1.32.2RSQLite2.0

rstudioapi

0.7

0.9.0

0.7

R.utils

2.8.0

2.5.0

rvest

0.3.2

rzmq

0.9.3

S4Vectors0.18.3

scales

0.5.0

1.0.0

0.5.0

selectr

0.3-1

0.4-1

0.3-1

sessioninfo

1.1.1

sfsmisc

1.1-1

shiny

1.3.0

1.0.5

1.0.5snow0.4-2

sourcetools

0.1.7

0.1.6

SparseM

1.77

spatial

7.3-11

splines

3.3.3

3.4.2

3.4.3

3.5.3

stats

3.3.3

3.4.2

3.4.3

3.5.3

stats4

3.3.3

3.4.2

3.4.3

3.5.3

stringi

1.1.6

1.1.5

1.1.6

1.4.3

1.1.5

stringr

1.2.0

1.4.0

1.2.0

survival

2.40-1

2.41-3

2.43-3

sys

3.1

tcltk

3.3.3

3.4.2

3.4.3

3.5.3

testthat

2.0.1

2.0.0

1.0.2

tibble

1.4.1

1.4.2

1.4.1

2.0.1

tidyr

0.7.2

0.8.0

0.7.2

0.8.3

0.7.2

tidyselect

0.2.3

0.2.5

0.2.3

tidyverse

1.2.1

timeDate

3042.101

tinytex

0.11

tools

3.3.3

3.4.2

3.4.3

3.5.3

TTR

0.23-2

usethis

1.4.0

utf8

1.1.3

1.1.2

1.1.4

1.1.3

utils

3.3.3

3.4.2

3.4.3

3.5.3

uuid

0.1-2

viridisLite

0.2.0

0.3.0

0.2.0

whisker

0.3-2

withr

2.1.2

2.1.1

2.1.2

xfun

0.6

0.5

XML3.98-1.9

xml2

1.1.1

1.2.0

1.1.1

1.2.0

1.1.1

xopen

1.0.0

xtable

1.8-3

1.8-2

xts

0.11-2

0.10-1

XVector0.20.0

yaml

2.1.16

2.1.14

2.1.16

2.2.0

2.1.14zlibbioc1.26.0

zoo

1.8-5

1.8-0

.3	2.3	2.3
gsubfn	0.7
gtable	0.3.0	0.3.0	0.3.0
gtools	3.8.1
haven	2.1.1	2.4.3	2.4.3
hdf5r	1.2.0
here		1.0.1	1.0.1
hexbin	1.27.3	1.28.2	1.28.2
highr	0.8	0.9	0.9
Hmisc	4.4-0
hms	0.5.0	1.1.1	1.1.1
htmlTable	1.13.1
htmltools	0.3.6	0.5.2	0.5.2
htmlwidgets	1.3	1.5.4	1.5.4
httpcode		0.3.0	0.3.0
httpuv	1.5.1	1.6.3	1.6.3
httr	1.4.1	1.4.2	1.4.2
hwriter	1.3.2
ica	1.0-2
ids		1.0.1	1.0.1
igraph	1.2.4.1	1.2.6	1.2.9
influenceR		0.1.0.1	0.1.0.1
ini	0.3.1
inline	0.3.15
ipred	0.9-9	0.9-12	0.9-12
IRanges	2.22.2
IRdisplay		1.0	1.0
IRkernel		1.2	1.2
irlba	2.3.3
isoband		0.2.5	0.2.5
iterators	1.0.12	1.0.13	1.0.13
janitor	1.2.0
jquerylib		0.1.4	0.1.4
jsonlite	1.6.1	1.7.2	1.7.2
kableExtra		1.3.4	1.3.4
KernSmooth	2.23-18	2.23-20	2.23-20
knitr	1.28	1.36	1.35
labeling	0.3	0.4.2	0.4.2
Lahman		9.0-0	9.0-0
lambda.r	1.2.3
later	0.8.0	1.2.0	1.2.0
lattice	0.20-41	0.20-45	0.20-45
latticeExtra	0.6-28
lava	1.6.6	1.6.10	1.6.10
lazyeval	0.2.2	0.2.2	0.2.2
leaflet		2.0.4.1	2.0.4.1
leaflet.providers		1.9.0	1.9.0
leiden	0.3.1
lifecycle		1.0.1	1.0.1
limma	3.40.6
listenv	0.7.0	0.8.0	0.8.0
lme4	1.1-21	1.1-27.1	1.1-27.1
lmtest	0.9-37
lobstr		1.1.1	1.1.1
locfit	1.5-9.1
loo	2.1.0
lsei	1.2-0
lubridate	1.7.4	1.8.0	1.8.0
magick	2.1	2.7.3	2.7.3
magrittr	1.5	2.0.1	2.0.1
maps	3.3.0	3.4.0	3.4.0
maptools		1.1-2	1.1-2
markdown	1.1	1.1	1.1
MASS	7.3-53.1	7.3-54	7.3-54
Matrix	1.3-2	1.3-4	1.3-4
MatrixModels		0.5-0	0.5-0
matrixStats	0.55.0	0.61.0	0.61.0
memoise	1.1.0		2.0.1
metap	1.1
methods	4.0.3	4.0.5	4.1.1
mgcv	1.8-34	1.8-38	1.8-38
mime	0.7	0.12	0.12
minqa	1.2.4	1.2.4	1.2.4
mlr	2.15.0
mnormt	1.5-5
ModelMetrics	1.2.2	1.2.2.2	1.2.2.2
modelr	0.1.5	0.1.8	0.1.8
multtest	2.40.0
munsell	0.5.0	0.5.0	0.5.0
ncdf4	1.16.1
nlme	3.1-152	3.1-150	3.1-153
nloptr	1.2.1	1.2.2.2	1.2.2.3
nnet	7.3-15	7.3-16	7.3-16
npsurv	0.4-0
numDeriv	2016.8-1.1	2016.8-1.1	2016.8-1.1
nycflights13		1.0.2	1.0.2
openssl	1.4.1	1.4.5	1.4.5
openxlsx	4.1.0.1	4.2.4	4.2.4
pacman	0.5.1	0.5.1	0.5.1
parallel	4.0.3	4.0.5	4.1.1
parallelly		1.29.0	1.29.0
parallelMap	1.4
ParamHelpers	1.12
pbapply	1.4-1
pbdZMQ		0.3-6	0.3-6
pbkrtest		0.5.1	0.5.1
pdftools		3.0.1	3.0.1
phangorn	2.5.5
phytools	0.6-99
pillar	1.4.2	1.6.4	1.6.4
pkgbuild	1.0.8
pkgconfig	2.0.2	2.0.3	2.0.3
pkgload	1.0.2	1.2.4	1.2.4
plogr	0.2.0
plotly	4.9.0	4.10.0	4.10.0
plotrix	3.7-6
plyr	1.8.4	1.8.6	1.8.6
png	0.1-7	0.1-7	0.1-7
polynom		1.4-0	1.4-0
praise	1.0.0	1.0.0	1.0.0
prettyunits	1.0.2	1.1.1	1.1.1
pROC		1.18.0	1.18.0
processx	3.4.1	3.5.2	3.5.2
prodlim	2018.04.18	2019.11.13	2019.11.13
progress	1.2.2	1.2.2	1.2.2
progressr		0.9.0	0.9.0
promises	1.0.1	1.2.0.1	1.2.0.1
proto	1.0.0
proxy		0.4-26	0.4-26
pryr	0.1.4	0.1.5	0.1.5
ps	1.3.0	1.6.0	1.6.0
purrr	0.3.4	0.3.4	0.3.4
qpdf		1.1	1.1
quadprog	1.5-7
quantmod	0.4-15	0.4.18	0.4.18
quantreg		5.86	5.86
qvalue	2.16.0
R.methodsS3	1.7.1
R.oo	1.23.0
R.utils	2.9.0
r2d3		0.2.5	0.2.5
R6	2.4.0	2.5.1	2.5.1
randomForest	4.6-14	4.6-14	4.6-14
RANN	2.6.1
rappdirs	0.3.1	0.3.3	0.3.3
raster		3.4-13	3.5-2
rbokeh	0.5.0	0.5.2	0.5.2
rcmdcheck	1.3.3
RColorBrewer	1.1-2	1.1-2	1.1-2
Rcpp	1.0.4.6	1.0.7	1.0.7
RcppAnnoy	0.0.12
RcppArmadillo	0.9.600.4.0	0.10.7.3.0	0.10.7.3.0
RcppEigen	0.3.3.5.0	0.3.3.9.1	0.3.3.9.1
RcppParallel	4.4.3
RcppProgress	0.4.1
RCurl	1.98-1.2	1.98-1.5	1.98-1.5
Rdpack	0.11-0
readr	1.3.1	2.1.1	2.1.1
readxl	1.3.1	1.3.1	1.3.1
recipes	0.1.6	0.1.17	0.1.17
rematch	1.0.1	1.0.1	1.0.1
rematch2	2.1.2	2.1.2	2.1.2
remotes	2.1.1	2.4.2	2.4.2
repr		1.1.3	1.1.3
reprex	0.3.0	2.0.1	2.0.1
reshape2	1.4.3	1.4.4	1.4.4
reticulate	1.15	1.22	1.22
rex	1.1.2
rgexf		0.16.2	0.16.2
rhdf5	2.28.1
Rhdf5lib	1.6.3
Rhtslib	1.18.1
rio		0.5.29	0.5.29
rjson		0.2.20	0.2.20
rlang	0.4.6	0.4.12	0.4.12
rmarkdown	1.14	2.11	2.11
ROCR	1.0-7
ROTS	1.12.0
roxygen2	7.1.0
rpart	4.1-15	4.1-15	4.1-15
RPostgreSQL	0.6-2
rprojroot	1.3-2	2.0.2	2.0.2
Rsamtools	2.2.1
RSpectra	0.15-0
RSQLite	2.1.2
rstan	2.19.2
rstatix		0.7.0	0.7.0
rstudioapi	0.11	0.13	0.13
rsvd	1.0.2
rtracklayer	1.44.4
Rtsne	0.15
rversions	2.0.1
rvest	0.3.4	1.0.2	1.0.2
S4Vectors	0.26.1
sass		0.4.0	0.4.0
scales	1.0.0	1.1.1	1.1.1
scatterplot3d	0.3-41
sctransform	0.2.0
SDMTools	1.1-221.1
selectr	0.4-1	0.4-2	0.4-2
servr		0.24	0.24
sessioninfo	1.1.1
Seurat	3.1.0
shape		1.4.6	1.4.6
shiny	1.3.2	1.7.1	1.7.1
sitmo	2.0.1
sm	2.2-5.6
snakecase	0.11.0
snow	0.4-3	0.4-4	0.4-4
sourcetools	0.1.7	0.1.7	0.1.7
sp		1.4-6	1.4-6
sparklyr		1.7.3	1.7.3
SparseM		1.81	1.81
spatial		7.3-14	7.3-14
splines	4.0.3	4.0.5	4.1.1
splitstackshape	1.4.8
sqldf	0.4-11
SQUAREM	2017.10-1	2021.1	2021.1
StanHeaders	2.18.1-10
statmod	1.4.32	1.4.36	1.4.36
stats	4.0.3	4.0.5	4.1.1
stats4	4.0.3	4.0.5	4.1.1
stringi	1.4.3	1.7.6	1.7.6
stringr	1.4.0	1.4.0	1.4.0
SummarizedExperiment	1.18.2
survival	3.2-7	3.2-13	3.2-13
svglite		2.0.0	2.0.0
sys	3.2	3.4	3.4
systemfonts		1.0.3	1.0.3
tcltk	4.0.3	4.0.5	4.1.1
terra			1.4-22
testthat	2.3.2	3.1.1	3.1.1
tibble	2.1.3	3.1.6	3.1.6
tidyr	0.8.3	1.1.4	1.1.4
tidyselect	0.2.5	1.1.1	1.1.1
tidyverse	1.2.1	1.3.1	1.3.1
timeDate	3043.102	3043.102	3043.102
tinytex	0.15	0.35	0.35
tools	4.0.3	4.0.5	4.1.1
triebeard		0.3.0	0.3.0
tsne	0.1-3
TTR	0.23-4	0.24.2	0.24.2
tweenr		1.0.2	1.0.2
tximport	1.12.3
tximportData	1.18.0
tzdb		0.2.0	0.2.0
urltools		1.7.3	1.7.3
usethis	1.6.1
utf8	1.1.4	1.2.2	1.2.2
utils	4.0.3	4.0.5	4.1.1
uuid		1.0-3	1.0-3
uwot	0.1.3
vctrs	0.2.0	0.3.8	0.3.8
vioplot	0.3.2
viridis	0.5.1	0.6.2	0.6.2
viridisLite	0.3.0	0.4.0	0.4.0
visNetwork		2.1.0	2.1.0
vroom		1.5.7	1.5.7
waldo		0.3.1	0.3.1
webshot		0.5.2	0.5.2
whisker	0.3-2
withr	2.2.0	2.4.3	2.4.3
xfun	0.8	0.28	0.28
XML	3.98-1.20	3.99-0.8	3.99-0.8
xml2	1.3.2	1.3.3	1.3.3
xopen	1.0.0
xtable	1.8-4	1.8-4	1.8-4
xts	0.11-2	0.12.1	0.12.1
XVector	0.24.0
yaml	2.2.0	2.2.1	2.2.1
zeallot	0.1.0
zip	2.0.3	2.2.0	2.2.0
zlibbioc	1.30.0
zoo	1.8-6	1.8-9	1.8-9

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