bash
docker run -it ghcr.io/vjcitn/yescdsbook:devel RCancer data science concepts for undergraduates
Package: YESCDSbook
Authors: Vincent Carey [aut, cre]
Compiled: 2023-12-13
Package version: 0.98.4
R version: R Under development (unstable) (2023-11-22 r85609)
BioC version: 3.19
License: MIT + file LICENSE
Welcome
This is the landing page of the BiocBook entitled βCancer data science concepts for undergraduatesβ
This book introduces the reader to the concepts mapped below:
The YESCDS R package includes data structures and functions used in this book.
Docker image
A Docker image built from this repository is available here:
π ghcr.io/vjcitn/yescdsbook π³
Get started now π
You can get access to all the packages used in this book in < 1 minute, using this command in a terminal:
RStudio Server
An RStudio Server instance can be initiated from the Docker image as follows:
bash
docker run \
--volume <local_folder>:<destination_folder> \
-e PASSWORD=OHCA \
-p 8787:8787 \
ghcr.io/vjcitn/yescdsbook:develThe initiated RStudio Server instance will be available at https://localhost:8787.
Acknowledgments
Contributors:
- Alexandru Mahmoud, Channing Division of Network Medicine, Mass General Brigham
- Brittany Michel, Dana-Farber Cancer Institute
- Latrice Landry, Perelman School of Medicine, University of Pennsylvania
- Karen Burns White, Dana-Farber Cancer Institute
- Vincent Carey, Channing Division of Network Medicine, Mass General Brigham
This project is supported in part by
NSF ACCESS Allocation BIR190004 βEngineering and disseminating a software and analysis ecosystem for genomic data scienceβ
Chan-Zuckerberg Initiative EOSS Diversity & Inclusiveness EOSS-DI-0000000033 βBioconductor: Sustaining a Worldwide Community of Genome Data Scientistsβ
National Cancer Institute 5U24CA180996-08 βCancer Genomics: Integrative and Scalable Solutions in R/Bioconductorβ
National Human Genome Research Institute 2U24HG004059-17 βBioconductor: An Open-Source, Open-Development Computing Resource for Genomicsβ
Session info
Click to expand π
sessioninfo::session_info(
installed.packages()[,"Package"],
include_base = TRUE
)
## β Session info ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
## setting value
## version R Under development (unstable) (2023-11-22 r85609)
## os Ubuntu 22.04.3 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate C
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2023-12-13
## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
##
## β Packages ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
## package * version date (UTC) lib source
## abind 1.4-5 2016-07-21 [2] CRAN (R 4.4.0)
## AnnotationDbi 1.65.2 2023-11-03 [2] Bioconductor
## AnnotationHub 3.11.1 2023-12-11 [2] Bioconductor 3.19 (R 4.4.0)
## askpass 1.2.0 2023-09-03 [2] CRAN (R 4.4.0)
## base * 4.4.0 2023-11-26 [3] local
## base64enc 0.1-3 2015-07-28 [2] CRAN (R 4.4.0)
## beeswarm 0.4.0 2021-06-01 [2] CRAN (R 4.4.0)
## Biobase 2.63.0 2023-10-24 [2] Bioconductor
## BiocBaseUtils 1.5.0 2023-10-24 [2] Bioconductor
## BiocFileCache 2.11.1 2023-10-26 [2] Bioconductor
## BiocGenerics 0.49.1 2023-11-01 [2] Bioconductor
## BiocManager 1.30.22 2023-08-08 [2] CRAN (R 4.4.0)
## BiocStyle 2.31.0 2023-10-24 [2] Bioconductor
## BiocVersion 3.19.1 2023-10-26 [2] Bioconductor
## Biostrings 2.71.1 2023-10-25 [2] Bioconductor
## bit 4.0.5 2022-11-15 [2] CRAN (R 4.4.0)
## bit64 4.0.5 2020-08-30 [2] CRAN (R 4.4.0)
## bitops 1.0-7 2021-04-24 [2] CRAN (R 4.4.0)
## blob 1.2.4 2023-03-17 [2] CRAN (R 4.4.0)
## bookdown 0.37 2023-12-01 [2] CRAN (R 4.4.0)
## boot 1.3-28.1 2022-11-22 [3] CRAN (R 4.4.0)
## brew 1.0-8 2022-09-29 [2] CRAN (R 4.4.0)
## brio 1.1.3 2021-11-30 [2] CRAN (R 4.4.0)
## bslib 0.6.1 2023-11-28 [2] CRAN (R 4.4.0)
## cachem 1.0.8 2023-05-01 [2] CRAN (R 4.4.0)
## callr 3.7.3 2022-11-02 [2] CRAN (R 4.4.0)
## class 7.3-22 2023-05-03 [3] CRAN (R 4.4.0)
## classInt 0.4-10 2023-09-05 [2] CRAN (R 4.4.0)
## cli 3.6.2 2023-12-11 [2] CRAN (R 4.4.0)
## clipr 0.8.0 2022-02-22 [2] CRAN (R 4.4.0)
## cluster 2.1.6 2023-12-01 [3] CRAN (R 4.4.0)
## codetools 0.2-19 2023-02-01 [3] CRAN (R 4.4.0)
## colorspace 2.1-0 2023-01-23 [2] CRAN (R 4.4.0)
## commonmark 1.9.0 2023-03-17 [2] CRAN (R 4.4.0)
## compiler 4.4.0 2023-11-26 [3] local
## cpp11 0.4.7 2023-12-02 [2] CRAN (R 4.4.0)
## crayon 1.5.2 2022-09-29 [2] CRAN (R 4.4.0)
## credentials 2.0.1 2023-09-06 [2] CRAN (R 4.4.0)
## crosstalk 1.2.1 2023-11-23 [2] CRAN (R 4.4.0)
## curatedTCGAData 1.25.0 2023-10-31 [2] Bioconductor
## curl 5.2.0 2023-12-08 [2] CRAN (R 4.4.0)
## data.table 1.14.10 2023-12-08 [2] CRAN (R 4.4.0)
## datasets * 4.4.0 2023-11-26 [3] local
## DBI 1.1.3 2022-06-18 [2] CRAN (R 4.4.0)
## dbplyr 2.4.0 2023-10-26 [2] CRAN (R 4.4.0)
## DelayedArray 0.29.0 2023-10-24 [2] Bioconductor
## desc 1.4.2 2022-09-08 [2] CRAN (R 4.4.0)
## devtools 2.4.5 2022-10-11 [2] CRAN (R 4.4.0)
## diffobj 0.3.5 2021-10-05 [2] CRAN (R 4.4.0)
## digest 0.6.33 2023-07-07 [2] CRAN (R 4.4.0)
## docopt 0.7.1 2020-06-24 [2] CRAN (R 4.4.0)
## downlit 0.4.3 2023-06-29 [2] CRAN (R 4.4.0)
## dplyr 1.1.4 2023-11-17 [2] CRAN (R 4.4.0)
## DT 0.31 2023-12-09 [2] CRAN (R 4.4.0)
## e1071 1.7-14 2023-12-06 [2] CRAN (R 4.4.0)
## ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.4.0)
## evaluate 0.23 2023-11-01 [2] CRAN (R 4.4.0)
## ExperimentHub 2.11.1 2023-12-11 [2] Bioconductor 3.19 (R 4.4.0)
## fansi 1.0.6 2023-12-08 [2] CRAN (R 4.4.0)
## farver 2.1.1 2022-07-06 [2] CRAN (R 4.4.0)
## fastmap 1.1.1 2023-02-24 [2] CRAN (R 4.4.0)
## filelock 1.0.3 2023-12-11 [2] CRAN (R 4.4.0)
## fontawesome 0.5.2 2023-08-19 [2] CRAN (R 4.4.0)
## forcats 1.0.0 2023-01-29 [2] CRAN (R 4.4.0)
## foreign 0.8-86 2023-11-28 [3] CRAN (R 4.4.0)
## fs 1.6.3 2023-07-20 [2] CRAN (R 4.4.0)
## generics 0.1.3 2022-07-05 [2] CRAN (R 4.4.0)
## GenomeInfoDb 1.39.1 2023-11-08 [2] Bioconductor
## GenomeInfoDbData 1.2.11 2023-12-13 [2] Bioconductor
## GenomicRanges 1.55.1 2023-10-29 [2] Bioconductor
## gert 2.0.1 2023-12-04 [2] CRAN (R 4.4.0)
## ggbeeswarm 0.7.2 2023-04-29 [2] CRAN (R 4.4.0)
## ggplot2 3.4.4 2023-10-12 [2] CRAN (R 4.4.0)
## gh 1.4.0 2023-02-22 [2] CRAN (R 4.4.0)
## gitcreds 0.1.2 2022-09-08 [2] CRAN (R 4.4.0)
## glue 1.6.2 2022-02-24 [2] CRAN (R 4.4.0)
## graphics * 4.4.0 2023-11-26 [3] local
## grDevices * 4.4.0 2023-11-26 [3] local
## grid 4.4.0 2023-11-26 [3] local
## gridExtra 2.3 2017-09-09 [2] CRAN (R 4.4.0)
## gtable 0.3.4 2023-08-21 [2] CRAN (R 4.4.0)
## HDF5Array 1.31.0 2023-10-24 [2] Bioconductor
## highr 0.10 2022-12-22 [2] CRAN (R 4.4.0)
## htmltools 0.5.7 2023-11-03 [2] CRAN (R 4.4.0)
## htmlwidgets 1.6.4 2023-12-06 [2] CRAN (R 4.4.0)
## httpuv 1.6.13 2023-12-06 [2] CRAN (R 4.4.0)
## httr 1.4.7 2023-08-15 [2] CRAN (R 4.4.0)
## httr2 1.0.0 2023-11-14 [2] CRAN (R 4.4.0)
## ini 0.3.1 2018-05-20 [2] CRAN (R 4.4.0)
## IRanges 2.37.0 2023-10-24 [2] Bioconductor
## isoband 0.2.7 2022-12-20 [2] CRAN (R 4.4.0)
## jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.4.0)
## jsonlite 1.8.8 2023-12-04 [2] CRAN (R 4.4.0)
## KEGGREST 1.43.0 2023-10-24 [2] Bioconductor
## KernSmooth 2.23-22 2023-07-10 [3] CRAN (R 4.4.0)
## knitr 1.45 2023-10-30 [2] CRAN (R 4.4.0)
## labeling 0.4.3 2023-08-29 [2] CRAN (R 4.4.0)
## later 1.3.2 2023-12-06 [2] CRAN (R 4.4.0)
## lattice 0.22-5 2023-10-24 [3] CRAN (R 4.4.0)
## lazyeval 0.2.2 2019-03-15 [2] CRAN (R 4.4.0)
## leaflet 2.2.1 2023-11-13 [2] CRAN (R 4.4.0)
## leaflet.providers 2.0.0 2023-10-17 [2] CRAN (R 4.4.0)
## lifecycle 1.0.4 2023-11-07 [2] CRAN (R 4.4.0)
## littler 0.3.18 2023-03-26 [2] CRAN (R 4.4.0)
## magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.4.0)
## MASS 7.3-60.1 2023-11-26 [3] local
## Matrix 1.6-4 2023-11-30 [3] CRAN (R 4.4.0)
## MatrixGenerics 1.15.0 2023-10-24 [2] Bioconductor
## matrixStats 1.2.0 2023-12-11 [2] CRAN (R 4.4.0)
## memoise 2.0.1 2021-11-26 [2] CRAN (R 4.4.0)
## methods * 4.4.0 2023-11-26 [3] local
## mgcv 1.9-0 2023-07-11 [3] CRAN (R 4.4.0)
## mime 0.12 2021-09-28 [2] CRAN (R 4.4.0)
## miniUI 0.1.1.1 2018-05-18 [2] CRAN (R 4.4.0)
## MultiAssayExperiment 1.29.0 2023-10-24 [2] Bioconductor
## munsell 0.5.0 2018-06-12 [2] CRAN (R 4.4.0)
## nlme 3.1-164 2023-11-27 [3] CRAN (R 4.4.0)
## nnet 7.3-19 2023-05-03 [3] CRAN (R 4.4.0)
## openssl 2.1.1 2023-09-25 [2] CRAN (R 4.4.0)
## parallel 4.4.0 2023-11-26 [3] local
## pillar 1.9.0 2023-03-22 [2] CRAN (R 4.4.0)
## pkgbuild 1.4.2 2023-06-26 [2] CRAN (R 4.4.0)
## pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.4.0)
## pkgdown 2.0.7 2022-12-14 [2] CRAN (R 4.4.0)
## pkgload 1.3.3 2023-09-22 [2] CRAN (R 4.4.0)
## plogr 0.2.0 2018-03-25 [2] CRAN (R 4.4.0)
## plotly 4.10.3 2023-10-21 [2] CRAN (R 4.4.0)
## png 0.1-8 2022-11-29 [2] CRAN (R 4.4.0)
## praise 1.0.0 2015-08-11 [2] CRAN (R 4.4.0)
## preprocessCore 1.65.0 2023-10-24 [2] Bioconductor
## prettyunits 1.2.0 2023-09-24 [2] CRAN (R 4.4.0)
## processx 3.8.2 2023-06-30 [2] CRAN (R 4.4.0)
## profvis 0.3.8 2023-05-02 [2] CRAN (R 4.4.0)
## promises 1.2.1 2023-08-10 [2] CRAN (R 4.4.0)
## proxy 0.4-27 2022-06-09 [2] CRAN (R 4.4.0)
## ps 1.7.5 2023-04-18 [2] CRAN (R 4.4.0)
## purrr 1.0.2 2023-08-10 [2] CRAN (R 4.4.0)
## R6 2.5.1 2021-08-19 [2] CRAN (R 4.4.0)
## ragg 1.2.6 2023-10-10 [2] CRAN (R 4.4.0)
## RaggedExperiment 1.27.0 2023-10-24 [2] Bioconductor
## rappdirs 0.3.3 2021-01-31 [2] CRAN (R 4.4.0)
## raster 3.6-26 2023-10-14 [2] CRAN (R 4.4.0)
## rcmdcheck 1.4.0 2021-09-27 [2] CRAN (R 4.4.0)
## RColorBrewer 1.1-3 2022-04-03 [2] CRAN (R 4.4.0)
## Rcpp 1.0.11 2023-07-06 [2] CRAN (R 4.4.0)
## RCurl 1.98-1.13 2023-11-02 [2] CRAN (R 4.4.0)
## rematch2 2.1.2 2020-05-01 [2] CRAN (R 4.4.0)
## remotes 2.4.2.1 2023-07-18 [2] CRAN (R 4.4.0)
## rhdf5 2.47.1 2023-11-29 [2] Bioconductor 3.19 (R 4.4.0)
## rhdf5filters 1.15.1 2023-11-06 [2] Bioconductor
## Rhdf5lib 1.25.1 2023-12-11 [2] Bioconductor 3.19 (R 4.4.0)
## rlang 1.1.2 2023-11-04 [2] CRAN (R 4.4.0)
## rmarkdown 2.25 2023-09-18 [2] CRAN (R 4.4.0)
## roxygen2 7.2.3 2022-12-08 [2] CRAN (R 4.4.0)
## rpart 4.1.23 2023-12-05 [3] CRAN (R 4.4.0)
## rprojroot 2.0.4 2023-11-05 [2] CRAN (R 4.4.0)
## RSQLite 2.3.4 2023-12-08 [2] CRAN (R 4.4.0)
## rstudioapi 0.15.0 2023-07-07 [2] CRAN (R 4.4.0)
## rversions 2.1.2 2022-08-31 [2] CRAN (R 4.4.0)
## s2 1.1.5 2023-12-10 [2] CRAN (R 4.4.0)
## S4Arrays 1.3.1 2023-11-27 [2] Bioconductor 3.19 (R 4.4.0)
## S4Vectors 0.41.2 2023-11-23 [2] Bioconductor 3.19 (R 4.4.0)
## sass 0.4.8 2023-12-06 [2] CRAN (R 4.4.0)
## scales 1.3.0 2023-11-28 [2] CRAN (R 4.4.0)
## sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.4.0)
## sf 1.0-14 2023-07-11 [2] CRAN (R 4.4.0)
## shiny 1.8.0 2023-11-17 [2] CRAN (R 4.4.0)
## sourcetools 0.1.7-1 2023-02-01 [2] CRAN (R 4.4.0)
## sp 2.1-2 2023-11-26 [2] CRAN (R 4.4.0)
## SparseArray 1.3.1 2023-11-07 [2] Bioconductor
## spatial 7.3-17 2023-07-20 [3] CRAN (R 4.4.0)
## splines 4.4.0 2023-11-26 [3] local
## stats * 4.4.0 2023-11-26 [3] local
## stats4 4.4.0 2023-11-26 [3] local
## stringi 1.8.3 2023-12-11 [2] CRAN (R 4.4.0)
## stringr 1.5.1 2023-11-14 [2] CRAN (R 4.4.0)
## SummarizedExperiment 1.33.1 2023-11-28 [2] Bioconductor 3.19 (R 4.4.0)
## survival 3.5-7 2023-08-14 [3] CRAN (R 4.4.0)
## sys 3.4.2 2023-05-23 [2] CRAN (R 4.4.0)
## systemfonts 1.0.5 2023-10-09 [2] CRAN (R 4.4.0)
## tcltk 4.4.0 2023-11-26 [3] local
## terra 1.7-55 2023-10-13 [2] CRAN (R 4.4.0)
## testthat 3.2.1 2023-12-02 [2] CRAN (R 4.4.0)
## textshaping 0.3.7 2023-10-09 [2] CRAN (R 4.4.0)
## tibble 3.2.1 2023-03-20 [2] CRAN (R 4.4.0)
## tidyr 1.3.0 2023-01-24 [2] CRAN (R 4.4.0)
## tidyselect 1.2.0 2022-10-10 [2] CRAN (R 4.4.0)
## tinytex 0.49 2023-11-22 [2] CRAN (R 4.4.0)
## tools 4.4.0 2023-11-26 [3] local
## units 0.8-5 2023-11-28 [2] CRAN (R 4.4.0)
## urlchecker 1.0.1 2021-11-30 [2] CRAN (R 4.4.0)
## usethis 2.2.2 2023-07-06 [2] CRAN (R 4.4.0)
## utf8 1.2.4 2023-10-22 [2] CRAN (R 4.4.0)
## utils * 4.4.0 2023-11-26 [3] local
## vctrs 0.6.5 2023-12-01 [2] CRAN (R 4.4.0)
## vipor 0.4.5 2017-03-22 [2] CRAN (R 4.4.0)
## viridis 0.6.4 2023-07-22 [2] CRAN (R 4.4.0)
## viridisLite 0.4.2 2023-05-02 [2] CRAN (R 4.4.0)
## waldo 0.5.2 2023-11-02 [2] CRAN (R 4.4.0)
## whisker 0.4.1 2022-12-05 [2] CRAN (R 4.4.0)
## withr 2.5.2 2023-10-30 [2] CRAN (R 4.4.0)
## wk 0.9.1 2023-11-29 [2] CRAN (R 4.4.0)
## xfun 0.41 2023-11-01 [2] CRAN (R 4.4.0)
## xml2 1.3.6 2023-12-04 [2] CRAN (R 4.4.0)
## xopen 1.0.0 2018-09-17 [2] CRAN (R 4.4.0)
## xtable 1.8-4 2019-04-21 [2] CRAN (R 4.4.0)
## XVector 0.43.0 2023-10-24 [2] Bioconductor
## yaml 2.3.8 2023-12-11 [2] CRAN (R 4.4.0)
## YESCDS 0.99.3 2023-12-13 [2] Github (vjcitn/YESCDS@26ad809)
## YESCDSbook 0.98.4 2023-12-13 [1] local
## zip 2.3.0 2023-04-17 [2] CRAN (R 4.4.0)
## zlibbioc 1.49.0 2023-10-24 [2] Bioconductor
##
## [1] /tmp/Rtmpt8bwcZ/Rinstb4a46155c
## [2] /usr/local/lib/R/site-library
## [3] /usr/local/lib/R/library
##
## βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ