5  Software

5.1 Installing R packages

The following code will download all the packages needed to run the analyses in this book.

Code

# Download EnvirOmix package if not already installed:
if(!requireNamespace("EnvirOmix", quietly = TRUE)){
  if(!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
  devtools::install_github("Goodrich-Lab/EnvirOmix")
}

# List all CRAN packages used in this book:
cran_packages <- c("tidyverse",
                   "tools",
                   "parallel",
                   "boot",
                   "table1",
                   "BiocManager",
                   "ggplot2",
                   "cowplot",
                   "ggh4x",
                   "LUCIDus",
                   "networkD3",
                   "plotly",
                   "htmlwidgets",
                   "jsonlite")

# Install cran packages if not already installed:
for(package_name in cran_packages){
  if(!requireNamespace(package_name, quietly = TRUE)){
    install.packages(package_name, repos = "http://cran.r-project.org/")
  }
}

# List all Bioconductor packages used in this book:
bioconductor_packages <- c("BiocGenerics", 
                           "ComplexHeatmap", 
                           "IRanges",
                           "S4Vectors")

# Install bioconductor packages if not already installed:
for(package_name in bioconductor_packages){
  if(!requireNamespace(package_name, quietly = TRUE)){
    BiocManager::install(package_name)
  }
}

5.2 R development environment

The following table lists the package versions and corresponding repository of all the R packages that were used to develop the code in this book.

List of all R Packages used in this book.

Package	Version	Attached or Loaded	Date/Publication	Source
ComplexHeatmap	2.16.0	Attached	2023-05-08	Bioconductor
cowplot	1.1.1	Attached	2020-12-30	CRAN (R 4.3.0)
devtools	2.4.5	Attached	2022-10-11	CRAN (R 4.3.0)
dplyr	1.1.3	Attached	2023-09-03	CRAN (R 4.3.0)
EnvirOmix	0.0.0.9000	Attached	2023-11-03	Bioconductor
forcats	1.0.0	Attached	2023-01-29	CRAN (R 4.3.0)
ggh4x	0.2.6	Attached	2023-08-30	CRAN (R 4.3.0)
ggplot2	3.4.4	Attached	2023-10-12	CRAN (R 4.3.1)
htmlwidgets	1.6.2	Attached	2023-03-17	CRAN (R 4.3.0)
jsonlite	1.8.7	Attached	2023-06-29	CRAN (R 4.3.0)
lubridate	1.9.3	Attached	2023-09-27	CRAN (R 4.3.1)
LUCIDus	3.0.1	Attached	2023-10-31	CRAN (R 4.3.1)
networkD3	0.4	Attached	2017-03-18	CRAN (R 4.3.0)
plotly	4.10.2	Attached	2023-06-03	CRAN (R 4.3.0)
purrr	1.0.2	Attached	2023-08-10	CRAN (R 4.3.0)
readr	2.1.4	Attached	2023-02-10	CRAN (R 4.3.0)
stringr	1.5.0	Attached	2022-12-02	CRAN (R 4.3.0)
table1	1.4.3	Attached	2023-01-06	CRAN (R 4.3.0)
tibble	3.2.1	Attached	2023-03-20	CRAN (R 4.3.0)
tidyr	1.3.0	Attached	2023-01-24	CRAN (R 4.3.0)
tidyverse	2.0.0	Attached	2023-02-22	CRAN (R 4.3.0)
usethis	2.2.2	Attached	2023-07-06	CRAN (R 4.3.0)
abind	1.4-5	Loaded	2016-07-21	CRAN (R 4.3.0)
adaptMCMC	1.4	Loaded	2021-03-29	CRAN (R 4.3.0)
arm	1.13-1	Loaded	2022-08-28	CRAN (R 4.3.0)
backports	1.4.1	Loaded	2021-12-13	CRAN (R 4.3.0)
BiocGenerics	0.46.0	Loaded	2023-06-04	Bioconductor
BiocManager	1.30.22	Loaded	2023-08-08	CRAN (R 4.3.0)
bitops	1.0-7	Loaded	2021-04-24	CRAN (R 4.3.0)
boot	1.3-28.1	Loaded	2022-11-22	CRAN (R 4.3.1)
broom	1.0.5	Loaded	2023-06-09	CRAN (R 4.3.0)
cachem	1.0.8	Loaded	2023-05-01	CRAN (R 4.3.0)
callr	3.7.3	Loaded	2022-11-02	CRAN (R 4.3.0)
caTools	1.18.2	Loaded	2021-03-28	CRAN (R 4.3.0)
circlize	0.4.15	Loaded	2022-05-10	CRAN (R 4.3.0)
class	7.3-22	Loaded	2023-05-03	CRAN (R 4.3.1)
cli	3.6.1	Loaded	2023-03-23	CRAN (R 4.3.0)
clue	0.3-65	Loaded	2023-09-23	CRAN (R 4.3.1)
cluster	2.1.4	Loaded	2022-08-22	CRAN (R 4.3.1)
coda	0.19-4	Loaded	2020-09-30	CRAN (R 4.3.0)
codetools	0.2-19	Loaded	2023-02-01	CRAN (R 4.3.1)
colorspace	2.1-0	Loaded	2023-01-23	CRAN (R 4.3.0)
conquer	1.3.3	Loaded	2023-03-06	CRAN (R 4.3.0)
crayon	1.5.2	Loaded	2022-09-29	CRAN (R 4.3.0)
data.table	1.14.8	Loaded	2023-02-17	CRAN (R 4.3.0)
digest	0.6.33	Loaded	2023-07-07	CRAN (R 4.3.0)
doParallel	1.0.17	Loaded	2022-02-07	CRAN (R 4.3.0)
e1071	1.7-13	Loaded	2023-02-01	CRAN (R 4.3.0)
ellipsis	0.3.2	Loaded	2021-04-29	CRAN (R 4.3.0)
epiomics	1.0.0	Loaded	2023-03-15	CRAN (R 4.3.0)
evaluate	0.23	Loaded	2023-11-01	CRAN (R 4.3.1)
fansi	1.0.5	Loaded	2023-10-08	CRAN (R 4.3.1)
fastmap	1.1.1	Loaded	2023-02-24	CRAN (R 4.3.0)
fdrtool	1.2.17	Loaded	2021-11-13	CRAN (R 4.3.0)
foreach	1.5.2	Loaded	2022-02-02	CRAN (R 4.3.0)
Formula	1.2-5	Loaded	2023-02-24	CRAN (R 4.3.0)
fs	1.6.3	Loaded	2023-07-20	CRAN (R 4.3.0)
generics	0.1.3	Loaded	2022-07-05	CRAN (R 4.3.0)
GetoptLong	1.0.5	Loaded	2020-12-15	CRAN (R 4.3.0)
ggrepel	0.9.4	Loaded	2023-10-13	CRAN (R 4.3.1)
glasso	1.11	Loaded	2019-10-01	CRAN (R 4.3.0)
glmnet	4.1-8	Loaded	2023-08-22	CRAN (R 4.3.0)
GlobalOptions	0.1.2	Loaded	2020-06-10	CRAN (R 4.3.0)
glue	1.6.2	Loaded	2022-02-24	CRAN (R 4.3.0)
gplots	3.1.3	Loaded	2022-04-25	CRAN (R 4.3.0)
gridExtra	2.3	Loaded	2017-09-09	CRAN (R 4.3.0)
gtable	0.3.4	Loaded	2023-08-21	CRAN (R 4.3.0)
gtools	3.9.4	Loaded	2022-11-27	CRAN (R 4.3.0)
hdi	0.1-9	Loaded	2021-05-27	CRAN (R 4.3.0)
HDMT	1.0.5	Loaded	2022-01-29	CRAN (R 4.3.0)
here	1.0.1	Loaded	2020-12-13	CRAN (R 4.3.0)
HIMA	2.2.1	Loaded	2023-09-10	CRAN (R 4.3.0)
hms	1.1.3	Loaded	2023-03-21	CRAN (R 4.3.0)
hommel	1.6	Loaded	2021-12-17	CRAN (R 4.3.0)
htmltools	0.5.6.1	Loaded	2023-10-06	CRAN (R 4.3.1)
httpuv	1.6.11	Loaded	2023-05-11	CRAN (R 4.3.0)
httr	1.4.7	Loaded	2023-08-15	CRAN (R 4.3.0)
igraph	1.5.1	Loaded	2023-08-10	CRAN (R 4.3.0)
intervals	0.15.4	Loaded	2023-06-29	CRAN (R 4.3.0)
IRanges	2.34.1	Loaded	2023-07-02	Bioconductor
iterators	1.0.14	Loaded	2022-02-05	CRAN (R 4.3.0)
KernSmooth	2.23-22	Loaded	2023-07-10	CRAN (R 4.3.0)
knitr	1.44	Loaded	2023-09-11	CRAN (R 4.3.0)
lars	1.3	Loaded	2022-04-13	CRAN (R 4.3.0)
later	1.3.1	Loaded	2023-05-02	CRAN (R 4.3.0)
lattice	0.21-9	Loaded	2023-10-01	CRAN (R 4.3.1)
lavaan	0.6-16	Loaded	2023-07-19	CRAN (R 4.3.0)
lazyeval	0.2.2	Loaded	2019-03-15	CRAN (R 4.3.0)
lbfgs	1.2.1.2	Loaded	2022-06-23	CRAN (R 4.3.0)
lifecycle	1.0.3	Loaded	2022-10-07	CRAN (R 4.3.0)
linprog	0.9-4	Loaded	2022-03-09	CRAN (R 4.3.0)
lme4	1.1-34	Loaded	2023-07-04	CRAN (R 4.3.0)
lmerTest	3.1-3	Loaded	2020-10-23	CRAN (R 4.3.0)
lpSolve	5.6.19	Loaded	2023-09-13	CRAN (R 4.3.0)
magrittr	2.0.3	Loaded	2022-03-30	CRAN (R 4.3.0)
MASS	7.3-60	Loaded	2023-05-04	CRAN (R 4.3.1)
Matrix	1.6-1.1	Loaded	2023-09-18	CRAN (R 4.3.1)
MatrixModels	0.5-2	Loaded	2023-07-10	CRAN (R 4.3.0)
matrixStats	1.0.0	Loaded	2023-06-02	CRAN (R 4.3.0)
mclust	6.0.0	Loaded	2022-10-31	CRAN (R 4.3.0)
memoise	2.0.1	Loaded	2021-11-26	CRAN (R 4.3.0)
mime	0.12	Loaded	2021-09-28	CRAN (R 4.3.0)
miniUI	0.1.1.1	Loaded	2018-05-18	CRAN (R 4.3.0)
minqa	1.2.6	Loaded	2023-09-11	CRAN (R 4.3.0)
mnormt	2.1.1	Loaded	2022-09-26	CRAN (R 4.3.0)
modelr	0.1.11	Loaded	2023-03-22	CRAN (R 4.3.0)
munsell	0.5.0	Loaded	2018-06-12	CRAN (R 4.3.0)
ncvreg	3.14.1	Loaded	2023-04-25	CRAN (R 4.3.0)
nlme	3.1-163	Loaded	2023-08-09	CRAN (R 4.3.0)
nloptr	2.0.3	Loaded	2022-05-26	CRAN (R 4.3.0)
nnet	7.3-19	Loaded	2023-05-03	CRAN (R 4.3.1)
numDeriv	2016.8-1.1	Loaded	2019-06-06	CRAN (R 4.3.0)
OpenMx	2.21.8	Loaded	2023-04-05	CRAN (R 4.3.0)
pbivnorm	0.6.0	Loaded	2015-01-23	CRAN (R 4.3.0)
pillar	1.9.0	Loaded	2023-03-22	CRAN (R 4.3.0)
pkgbuild	1.4.2	Loaded	2023-06-26	CRAN (R 4.3.0)
pkgconfig	2.0.3	Loaded	2019-09-22	CRAN (R 4.3.0)
pkgload	1.3.3	Loaded	2023-09-22	CRAN (R 4.3.1)
plyr	1.8.9	Loaded	2023-10-02	CRAN (R 4.3.1)
png	0.1-8	Loaded	2022-11-29	CRAN (R 4.3.0)
prettyunits	1.2.0	Loaded	2023-09-24	CRAN (R 4.3.1)
processx	3.8.2	Loaded	2023-06-30	CRAN (R 4.3.0)
profvis	0.3.8	Loaded	2023-05-02	CRAN (R 4.3.0)
progress	1.2.2	Loaded	2019-05-16	CRAN (R 4.3.0)
promises	1.2.1	Loaded	2023-08-10	CRAN (R 4.3.0)
proxy	0.4-27	Loaded	2022-06-09	CRAN (R 4.3.0)
ps	1.7.5	Loaded	2023-04-18	CRAN (R 4.3.0)
pscl	1.5.5.1	Loaded	2023-05-10	CRAN (R 4.3.0)
qgcomp	2.15.2	Loaded	2023-08-10	CRAN (R 4.3.0)
quadprog	1.5-8	Loaded	2019-11-20	CRAN (R 4.3.0)
quantreg	5.97	Loaded	2023-08-19	CRAN (R 4.3.0)
qvalue	2.34.0	Loaded	2023-10-26	Bioconductor
r.jive	2.4	Loaded	2020-11-17	CRAN (R 4.3.0)
R6	2.5.1	Loaded	2021-08-19	CRAN (R 4.3.0)
RColorBrewer	1.1-3	Loaded	2022-04-03	CRAN (R 4.3.0)
Rcpp	1.0.11	Loaded	2023-07-06	CRAN (R 4.3.0)
RcppParallel	5.1.7	Loaded	2023-02-27	CRAN (R 4.3.0)
remotes	2.4.2.1	Loaded	2023-07-18	CRAN (R 4.3.0)
reshape2	1.4.4	Loaded	2020-04-09	CRAN (R 4.3.0)
rjson	0.2.21	Loaded	2022-01-09	CRAN (R 4.3.0)
rlang	1.1.1	Loaded	2023-04-28	CRAN (R 4.3.0)
rmarkdown	2.25	Loaded	2023-09-18	CRAN (R 4.3.1)
RMediation	1.2.2	Loaded	2023-05-12	CRAN (R 4.3.0)
rprojroot	2.0.3	Loaded	2022-04-02	CRAN (R 4.3.0)
rstudioapi	0.15.0	Loaded	2023-07-07	CRAN (R 4.3.0)
S4Vectors	0.38.2	Loaded	2023-09-24	Bioconductor
scales	1.2.1	Loaded	2022-08-20	CRAN (R 4.3.0)
scalreg	1.0.1	Loaded	2019-01-25	CRAN (R 4.3.0)
selectiveInference	1.2.5	Loaded	2019-09-07	CRAN (R 4.3.0)
sessioninfo	1.2.2	Loaded	2021-12-06	CRAN (R 4.3.0)
shape	1.4.6	Loaded	2021-05-19	CRAN (R 4.3.0)
shiny	1.7.5.1	Loaded	2023-10-14	CRAN (R 4.3.1)
SparseM	1.81	Loaded	2021-02-18	CRAN (R 4.3.0)
stringi	1.7.12	Loaded	2023-01-11	CRAN (R 4.3.0)
survival	3.5-7	Loaded	2023-08-14	CRAN (R 4.3.0)
tidyselect	1.2.0	Loaded	2022-10-10	CRAN (R 4.3.0)
timechange	0.2.0	Loaded	2023-01-11	CRAN (R 4.3.0)
tzdb	0.4.0	Loaded	2023-05-12	CRAN (R 4.3.0)
urlchecker	1.0.1	Loaded	2021-11-30	CRAN (R 4.3.0)
utf8	1.2.4	Loaded	2023-10-22	CRAN (R 4.3.1)
vctrs	0.6.4	Loaded	2023-10-12	CRAN (R 4.3.1)
viridisLite	0.4.2	Loaded	2023-05-02	CRAN (R 4.3.0)
withr	2.5.2	Loaded	2023-10-30	CRAN (R 4.3.1)
xfun	0.40	Loaded	2023-08-09	CRAN (R 4.3.0)
xtable	1.8-4	Loaded	2019-04-21	CRAN (R 4.3.0)
xtune	2.0.0	Loaded	2023-06-18	CRAN (R 4.3.0)
yaml	2.3.7	Loaded	2023-01-23	CRAN (R 4.3.0)

5.3 Software Environment

This book was developed on the following platform.

Setting	Value
version	R version 4.3.1 (2023-06-16)
os	macOS Sonoma 14.1
system	aarch64, darwin20
ui	X11
language	(EN)
collate	en_US.UTF-8
ctype	en_US.UTF-8
tz	America/Los_Angeles
date	2023-11-02
pandoc	3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)