bash
docker run -it ghcr.io/lmweber/osta:devel RPreamble
Package: OSTA
Compiled: 2025-02-01
Package version: 0.99.0
R version: R Under development (unstable) (2025-01-28 r87664)
Bioconductor version: 3.21
License: CC BY 4.0
Docker image
A Docker image built from this repository is available here: ghcr.io/lmweber/osta
Get started now
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/lmweber/osta:develThe initiated RStudio Server instance will be available at: https://localhost:8787
BiocBook
This book is built using the BiocBook package, developed by Jacques Serizay for building Quarto books with Bioconductor.
More details on how to build a book using BiocBook can be found in the BiocBook book.
Session info
Click to expand
sessioninfo::session_info(
installed.packages()[,"Package"],
include_base = TRUE
)## ─ Session info ────────────────────────────────────────────────────────────
## setting value
## version R Under development (unstable) (2025-01-28 r87664)
## os Ubuntu 24.04.1 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate C
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2025-02-01
## pandoc 3.6.2 @ /usr/bin/ (via rmarkdown)
##
## ─ Packages ────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
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## AnnotationDbi 1.69.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## AnnotationHub 3.15.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## askpass 1.2.1 2024-10-04 [2] CRAN (R 4.5.0)
## assorthead 1.1.13 2025-01-17 [2] Bioconductor 3.21 (R 4.5.0)
## attempt 0.3.1 2020-05-03 [2] CRAN (R 4.5.0)
## base * 4.5.0 2025-01-29 [3] local
## base64enc 0.1-3 2015-07-28 [2] CRAN (R 4.5.0)
## beachmat 2.23.6 2024-12-22 [2] Bioconductor 3.21 (R 4.5.0)
## beeswarm 0.4.0 2021-06-01 [2] CRAN (R 4.5.0)
## benchmarkme 1.0.8 2022-06-12 [2] CRAN (R 4.5.0)
## benchmarkmeData 1.0.4 2020-04-23 [2] CRAN (R 4.5.0)
## BH 1.87.0-1 2024-12-17 [2] CRAN (R 4.5.0)
## Biobase 2.67.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## BiocFileCache 2.15.1 2025-01-17 [2] Bioconductor 3.21 (R 4.5.0)
## BiocGenerics 0.53.6 2025-01-27 [2] Bioconductor 3.21 (R 4.5.0)
## BiocIO 1.17.1 2024-11-21 [2] Bioconductor 3.21 (R 4.5.0)
## BiocManager 1.30.25 2024-08-28 [2] CRAN (R 4.5.0)
## BiocNeighbors 2.1.2 2024-12-09 [2] Bioconductor 3.21 (R 4.5.0)
## BiocParallel 1.41.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## BiocSingular 1.23.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## BiocStyle 2.35.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## BiocVersion 3.21.1 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## Biostrings 2.75.3 2024-12-15 [2] Bioconductor 3.21 (R 4.5.0)
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## bit64 4.6.0-1 2025-01-16 [2] CRAN (R 4.5.0)
## bitops 1.0-9 2024-10-03 [2] CRAN (R 4.5.0)
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## bookdown 0.42 2025-01-07 [2] CRAN (R 4.5.0)
## boot 1.3-31 2024-08-28 [3] CRAN (R 4.5.0)
## brew 1.0-10 2023-12-16 [2] CRAN (R 4.5.0)
## brio 1.1.5 2024-04-24 [2] CRAN (R 4.5.0)
## BRISC 1.0.6 2024-10-02 [2] CRAN (R 4.5.0)
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## cachem 1.1.0 2024-05-16 [2] CRAN (R 4.5.0)
## Cairo 1.6-2 2023-11-28 [2] CRAN (R 4.5.0)
## callr 3.7.6 2024-03-25 [2] CRAN (R 4.5.0)
## circlize 0.4.16 2024-02-20 [2] CRAN (R 4.5.0)
## class 7.3-23 2025-01-01 [3] CRAN (R 4.5.0)
## cli 3.6.3 2024-06-21 [2] CRAN (R 4.5.0)
## clipr 0.8.0 2022-02-22 [2] CRAN (R 4.5.0)
## clue 0.3-66 2024-11-13 [2] CRAN (R 4.5.0)
## cluster 2.1.8 2024-12-11 [3] CRAN (R 4.5.0)
## codetools 0.2-20 2024-03-31 [3] CRAN (R 4.5.0)
## colorspace 2.1-1 2024-07-26 [2] CRAN (R 4.5.0)
## commonmark 1.9.2 2024-10-04 [2] CRAN (R 4.5.0)
## compiler 4.5.0 2025-01-29 [3] local
## ComplexHeatmap 2.23.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## config 0.3.2 2023-08-30 [2] CRAN (R 4.5.0)
## cowplot 1.1.3 2024-01-22 [2] CRAN (R 4.5.0)
## cpp11 0.5.1 2024-12-04 [2] CRAN (R 4.5.0)
## crayon 1.5.3 2024-06-20 [2] CRAN (R 4.5.0)
## credentials 2.0.2 2024-10-04 [2] CRAN (R 4.5.0)
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## curl 6.2.0 2025-01-23 [2] CRAN (R 4.5.0)
## data.table 1.16.4 2024-12-06 [2] CRAN (R 4.5.0)
## datasets * 4.5.0 2025-01-29 [3] local
## DBI 1.2.3 2024-06-02 [2] CRAN (R 4.5.0)
## dbplyr 2.5.0 2024-03-19 [2] CRAN (R 4.5.0)
## DelayedArray 0.33.4 2025-01-19 [2] Bioconductor 3.21 (R 4.5.0)
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## devtools 2.4.5 2022-10-11 [2] CRAN (R 4.5.0)
## diffobj 0.3.5 2021-10-05 [2] CRAN (R 4.5.0)
## digest 0.6.37 2024-08-19 [2] CRAN (R 4.5.0)
## docopt 0.7.1 2020-06-24 [2] CRAN (R 4.5.0)
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## dplyr 1.1.4 2023-11-17 [2] CRAN (R 4.5.0)
## dqrng 0.4.1 2024-05-28 [2] CRAN (R 4.5.0)
## DT 0.33 2024-04-04 [2] CRAN (R 4.5.0)
## edgeR 4.5.2 2025-01-24 [2] Bioconductor 3.21 (R 4.5.0)
## ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.5.0)
## evaluate 1.0.3 2025-01-10 [2] CRAN (R 4.5.0)
## ExperimentHub 2.15.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## fansi 1.0.6 2023-12-08 [2] CRAN (R 4.5.0)
## farver 2.1.2 2024-05-13 [2] CRAN (R 4.5.0)
## fastmap 1.2.0 2024-05-15 [2] CRAN (R 4.5.0)
## filelock 1.0.3 2023-12-11 [2] CRAN (R 4.5.0)
## FNN 1.1.4.1 2024-09-22 [2] CRAN (R 4.5.0)
## fontawesome 0.5.3 2024-11-16 [2] CRAN (R 4.5.0)
## foreach 1.5.2 2022-02-02 [2] CRAN (R 4.5.0)
## foreign 0.8-88 2025-01-12 [3] CRAN (R 4.5.0)
## formatR 1.14 2023-01-17 [2] CRAN (R 4.5.0)
## fs 1.6.5 2024-10-30 [2] CRAN (R 4.5.0)
## futile.logger 1.4.3 2016-07-10 [2] CRAN (R 4.5.0)
## futile.options 1.0.1 2018-04-20 [2] CRAN (R 4.5.0)
## generics 0.1.3 2022-07-05 [2] CRAN (R 4.5.0)
## GenomeInfoDb 1.43.4 2025-01-24 [2] Bioconductor 3.21 (R 4.5.0)
## GenomeInfoDbData 1.2.13 2025-02-01 [2] Bioconductor
## GenomicAlignments 1.43.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## GenomicRanges 1.59.1 2024-11-15 [2] Bioconductor 3.21 (R 4.5.0)
## gert 2.1.4 2024-10-14 [2] CRAN (R 4.5.0)
## GetoptLong 1.0.5 2020-12-15 [2] CRAN (R 4.5.0)
## ggbeeswarm 0.7.2 2023-04-29 [2] CRAN (R 4.5.0)
## ggplot2 3.5.1 2024-04-23 [2] CRAN (R 4.5.0)
## ggrastr 1.0.2 2023-06-01 [2] CRAN (R 4.5.0)
## ggrepel 0.9.6 2024-09-07 [2] CRAN (R 4.5.0)
## ggside 0.3.1 2024-03-01 [2] CRAN (R 4.5.0)
## ggspavis 1.13.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## gh 1.4.1 2024-03-28 [2] CRAN (R 4.5.0)
## gitcreds 0.1.2 2022-09-08 [2] CRAN (R 4.5.0)
## GlobalOptions 0.1.2 2020-06-10 [2] CRAN (R 4.5.0)
## glue 1.8.0 2024-09-30 [2] CRAN (R 4.5.0)
## golem 0.5.1 2024-08-27 [2] CRAN (R 4.5.0)
## graphics * 4.5.0 2025-01-29 [3] local
## grDevices * 4.5.0 2025-01-29 [3] local
## grid 4.5.0 2025-01-29 [3] local
## gridExtra 2.3 2017-09-09 [2] CRAN (R 4.5.0)
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## htmlwidgets 1.6.4 2023-12-06 [2] CRAN (R 4.5.0)
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## httr 1.4.7 2023-08-15 [2] CRAN (R 4.5.0)
## httr2 1.1.0 2025-01-18 [2] CRAN (R 4.5.0)
## igraph 2.1.4 2025-01-23 [2] CRAN (R 4.5.0)
## ini 0.3.1 2018-05-20 [2] CRAN (R 4.5.0)
## IRanges 2.41.2 2024-12-03 [2] Bioconductor 3.21 (R 4.5.0)
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## jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.5.0)
## jsonlite 1.8.9 2024-09-20 [2] CRAN (R 4.5.0)
## KEGGREST 1.47.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## KernSmooth 2.23-26 2025-01-01 [3] CRAN (R 4.5.0)
## knitr 1.49 2024-11-08 [2] CRAN (R 4.5.0)
## labeling 0.4.3 2023-08-29 [2] CRAN (R 4.5.0)
## lambda.r 1.2.4 2019-09-18 [2] CRAN (R 4.5.0)
## later 1.4.1 2024-11-27 [2] CRAN (R 4.5.0)
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## lazyeval 0.2.2 2019-03-15 [2] CRAN (R 4.5.0)
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## limma 3.63.3 2025-01-09 [2] Bioconductor 3.21 (R 4.5.0)
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## magick 2.8.5 2024-09-20 [2] CRAN (R 4.5.0)
## magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.5.0)
## MASS 7.3-64 2025-01-04 [3] CRAN (R 4.5.0)
## Matrix 1.7-2 2025-01-23 [3] CRAN (R 4.5.0)
## MatrixGenerics 1.19.1 2025-01-09 [2] Bioconductor 3.21 (R 4.5.0)
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## memoise 2.0.1 2021-11-26 [2] CRAN (R 4.5.0)
## metapod 1.15.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## methods * 4.5.0 2025-01-29 [3] local
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## nnSVG 1.11.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
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## OSTA 0.99.0 2025-02-01 [1] Bioconductor
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## parallel 4.5.0 2025-01-29 [3] local
## pbapply 1.7-2 2023-06-27 [2] CRAN (R 4.5.0)
## pheatmap 1.0.12 2019-01-04 [2] CRAN (R 4.5.0)
## pillar 1.10.1 2025-01-07 [2] CRAN (R 4.5.0)
## pkgbuild 1.4.6 2025-01-16 [2] CRAN (R 4.5.0)
## pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.5.0)
## pkgdown 2.1.1 2024-09-17 [2] CRAN (R 4.5.0)
## pkgload 1.4.0 2024-06-28 [2] CRAN (R 4.5.0)
## plogr 0.2.0 2018-03-25 [2] CRAN (R 4.5.0)
## plotly 4.10.4 2024-01-13 [2] CRAN (R 4.5.0)
## png 0.1-8 2022-11-29 [2] CRAN (R 4.5.0)
## praise 1.0.0 2015-08-11 [2] CRAN (R 4.5.0)
## preprocessCore 1.69.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
## prettyunits 1.2.0 2023-09-24 [2] CRAN (R 4.5.0)
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## profvis 0.4.0 2024-09-20 [2] CRAN (R 4.5.0)
## promises 1.3.2 2024-11-28 [2] CRAN (R 4.5.0)
## ps 1.8.1 2024-10-28 [2] CRAN (R 4.5.0)
## purrr 1.0.2 2023-08-10 [2] CRAN (R 4.5.0)
## R6 2.5.1 2021-08-19 [2] CRAN (R 4.5.0)
## ragg 1.3.3 2024-09-11 [2] CRAN (R 4.5.0)
## RANN 2.6.2 2024-08-25 [2] CRAN (R 4.5.0)
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## rcmdcheck 1.4.0 2021-09-27 [2] CRAN (R 4.5.0)
## RColorBrewer 1.1-3 2022-04-03 [2] CRAN (R 4.5.0)
## Rcpp 1.0.14 2025-01-12 [2] CRAN (R 4.5.0)
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## RcppEigen 0.3.4.0.2 2024-08-24 [2] CRAN (R 4.5.0)
## RcppML 0.3.7 2021-09-21 [2] CRAN (R 4.5.0)
## RcppProgress 0.4.2 2020-02-06 [2] CRAN (R 4.5.0)
## RCurl 1.98-1.16 2024-07-11 [2] CRAN (R 4.5.0)
## rdist 0.0.5 2020-05-04 [2] CRAN (R 4.5.0)
## rematch2 2.1.2 2020-05-01 [2] CRAN (R 4.5.0)
## remotes 2.5.0 2024-03-17 [2] CRAN (R 4.5.0)
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## rmarkdown 2.29 2024-11-04 [2] CRAN (R 4.5.0)
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## Rsamtools 2.23.1 2024-11-27 [2] Bioconductor 3.21 (R 4.5.0)
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## Rtsne 0.17 2023-12-07 [2] CRAN (R 4.5.0)
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## S4Vectors 0.45.2 2024-11-15 [2] Bioconductor 3.21 (R 4.5.0)
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## ScaledMatrix 1.15.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
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## SingleCellExperiment 1.29.1 2024-11-10 [2] Bioconductor 3.21 (R 4.5.0)
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## SparseArray 1.7.4 2025-01-17 [2] Bioconductor 3.21 (R 4.5.0)
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## tibble 3.2.1 2023-03-20 [2] CRAN (R 4.5.0)
## tidyr 1.3.1 2024-01-24 [2] CRAN (R 4.5.0)
## tidyselect 1.2.1 2024-03-11 [2] CRAN (R 4.5.0)
## tinytex 0.54 2024-11-01 [2] CRAN (R 4.5.0)
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## UCSC.utils 1.3.1 2025-01-15 [2] Bioconductor 3.21 (R 4.5.0)
## urlchecker 1.0.1 2021-11-30 [2] CRAN (R 4.5.0)
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## utf8 1.2.4 2023-10-22 [2] CRAN (R 4.5.0)
## utils * 4.5.0 2025-01-29 [3] local
## uwot 0.2.2 2024-04-21 [2] CRAN (R 4.5.0)
## vctrs 0.6.5 2023-12-01 [2] CRAN (R 4.5.0)
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## viridis 0.6.5 2024-01-29 [2] CRAN (R 4.5.0)
## viridisLite 0.4.2 2023-05-02 [2] CRAN (R 4.5.0)
## waldo 0.6.1 2024-11-07 [2] CRAN (R 4.5.0)
## whisker 0.4.1 2022-12-05 [2] CRAN (R 4.5.0)
## withr 3.0.2 2024-10-28 [2] CRAN (R 4.5.0)
## xfun 0.50 2025-01-07 [2] CRAN (R 4.5.0)
## XML 3.99-0.18 2025-01-01 [2] CRAN (R 4.5.0)
## xml2 1.3.6 2023-12-04 [2] CRAN (R 4.5.0)
## xopen 1.0.1 2024-04-25 [2] CRAN (R 4.5.0)
## xtable 1.8-4 2019-04-21 [2] CRAN (R 4.5.0)
## XVector 0.47.2 2025-01-08 [2] Bioconductor 3.21 (R 4.5.0)
## yaml 2.3.10 2024-07-26 [2] CRAN (R 4.5.0)
## zip 2.3.1 2024-01-27 [2] CRAN (R 4.5.0)
## zlibbioc 1.53.0 2024-10-29 [2] Bioconductor 3.21 (R 4.5.0)
##
## [1] /tmp/Rtmpefxe0i/Rinst8c34e965ec
## [2] /usr/local/lib/R/site-library
## [3] /usr/local/lib/R/library
##
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