Final R Session
This is the final R session after all the code in this book is run sequentially.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.3.0 (2023-04-21)
#> os Ubuntu 22.04.2 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz UTC
#> date 2023-07-11
#> pandoc 2.19.2 @ /usr/local/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> airway * 1.20.0 2023-04-27 [1] Bioconductor
#> AnnotationDbi 1.62.2 2023-07-02 [1] Bioconductor
#> AnnotationHub 3.8.0 2023-04-25 [1] Bioconductor
#> aod 1.3.2 2022-04-02 [1] RSPM (R 4.3.0)
#> attempt 0.3.1 2020-05-03 [1] RSPM (R 4.3.0)
#> backports 1.4.1 2021-12-13 [1] RSPM (R 4.3.0)
#> base64enc 0.1-3 2015-07-28 [2] RSPM (R 4.3.0)
#> beachmat 2.16.0 2023-04-25 [1] Bioconductor
#> beeswarm 0.4.0 2021-06-01 [1] RSPM (R 4.3.0)
#> benchmarkme 1.0.8 2022-06-12 [1] RSPM (R 4.3.0)
#> benchmarkmeData 1.0.4 2020-04-23 [1] RSPM (R 4.3.0)
#> bibtex 0.5.1 2023-01-26 [1] RSPM (R 4.3.0)
#> Biobase * 2.60.0 2023-04-25 [1] Bioconductor
#> BiocFileCache * 2.8.0 2023-04-25 [1] Bioconductor
#> BiocGenerics * 0.46.0 2023-04-25 [1] Bioconductor
#> BiocIO 1.10.0 2023-04-25 [1] Bioconductor
#> BiocManager 1.30.21 2023-06-10 [1] RSPM (R 4.3.0)
#> BiocNeighbors 1.18.0 2023-04-25 [1] Bioconductor
#> BiocParallel * 1.34.2 2023-05-22 [1] Bioconductor
#> BiocSingular 1.16.0 2023-04-25 [1] Bioconductor
#> BiocStyle * 2.28.0 2023-04-25 [1] Bioconductor
#> biocthis * 1.10.3 2023-06-07 [1] Bioconductor
#> BiocVersion 3.17.1 2022-11-04 [2] Bioconductor
#> Biostrings 2.68.1 2023-05-16 [1] Bioconductor
#> bit 4.0.5 2022-11-15 [1] RSPM (R 4.3.0)
#> bit64 4.0.5 2020-08-30 [1] RSPM (R 4.3.0)
#> bitops 1.0-7 2021-04-24 [1] RSPM (R 4.3.0)
#> blob 1.2.4 2023-03-17 [1] RSPM (R 4.3.0)
#> bookdown 0.34 2023-05-09 [1] RSPM (R 4.3.0)
#> boot 1.3-28.1 2022-11-22 [3] CRAN (R 4.3.0)
#> broom 1.0.5 2023-06-09 [1] RSPM (R 4.3.0)
#> bslib 0.5.0 2023-06-09 [2] RSPM (R 4.3.0)
#> cachem 1.0.8 2023-05-01 [2] RSPM (R 4.3.0)
#> Cairo 1.6-0 2022-07-05 [1] RSPM (R 4.3.0)
#> caTools 1.18.2 2021-03-28 [1] RSPM (R 4.3.0)
#> checkmate 2.2.0 2023-04-27 [1] RSPM (R 4.3.0)
#> circlize * 0.4.15 2022-05-10 [1] RSPM (R 4.3.0)
#> cli 3.6.1 2023-03-23 [2] RSPM (R 4.3.0)
#> clue 0.3-64 2023-01-31 [1] RSPM (R 4.3.0)
#> cluster 2.1.4 2022-08-22 [3] CRAN (R 4.3.0)
#> codetools 0.2-19 2023-02-01 [3] CRAN (R 4.3.0)
#> colorspace 2.1-0 2023-01-23 [1] RSPM (R 4.3.0)
#> colourpicker 1.2.0 2022-10-28 [1] RSPM (R 4.3.0)
#> ComplexHeatmap * 2.16.0 2023-04-25 [1] Bioconductor
#> config 0.3.1 2020-12-17 [1] RSPM (R 4.3.0)
#> cowplot * 1.1.1 2020-12-30 [1] RSPM (R 4.3.0)
#> crayon 1.5.2 2022-09-29 [2] RSPM (R 4.3.0)
#> curl 5.0.1 2023-06-07 [2] RSPM (R 4.3.0)
#> data.table 1.14.8 2023-02-17 [1] RSPM (R 4.3.0)
#> DBI 1.1.3 2022-06-18 [1] RSPM (R 4.3.0)
#> dbplyr * 2.3.3 2023-07-07 [1] RSPM (R 4.3.0)
#> DelayedArray 0.26.6 2023-07-02 [1] Bioconductor
#> DelayedMatrixStats 1.22.1 2023-06-09 [1] Bioconductor
#> digest 0.6.33 2023-07-07 [2] RSPM (R 4.3.0)
#> doParallel 1.0.17 2022-02-07 [1] RSPM (R 4.3.0)
#> dotCall64 1.0-2 2022-10-03 [1] RSPM (R 4.3.0)
#> dplyr 1.1.2 2023-04-20 [1] RSPM (R 4.3.0)
#> dqrng 0.3.0 2021-05-01 [1] RSPM (R 4.3.0)
#> DropletUtils 1.20.0 2023-04-25 [1] Bioconductor
#> DT 0.28 2023-05-18 [1] RSPM (R 4.3.0)
#> edgeR * 3.42.4 2023-05-31 [1] Bioconductor
#> ellipsis 0.3.2 2021-04-29 [2] RSPM (R 4.3.0)
#> EnvStats 2.8.0 2023-07-08 [1] RSPM (R 4.3.0)
#> evaluate 0.21 2023-05-05 [2] RSPM (R 4.3.0)
#> ExperimentHub 2.8.0 2023-04-25 [1] Bioconductor
#> ExploreModelMatrix * 1.12.0 2023-04-25 [1] Bioconductor
#> fansi 1.0.4 2023-01-22 [2] RSPM (R 4.3.0)
#> farver 2.1.1 2022-07-06 [1] RSPM (R 4.3.0)
#> fastmap 1.1.1 2023-02-24 [2] RSPM (R 4.3.0)
#> fields 14.1 2022-08-12 [1] RSPM (R 4.3.0)
#> filelock 1.0.2 2018-10-05 [1] RSPM (R 4.3.0)
#> foreach 1.5.2 2022-02-02 [1] RSPM (R 4.3.0)
#> foreign 0.8-84 2022-12-06 [3] CRAN (R 4.3.0)
#> Formula 1.2-5 2023-02-24 [1] RSPM (R 4.3.0)
#> fs 1.6.2 2023-04-25 [2] RSPM (R 4.3.0)
#> generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0)
#> GenomeInfoDb * 1.36.1 2023-06-21 [1] Bioconductor
#> GenomeInfoDbData 1.2.10 2023-05-17 [1] Bioconductor
#> GenomicAlignments 1.36.0 2023-04-25 [1] Bioconductor
#> GenomicRanges * 1.52.0 2023-04-25 [1] Bioconductor
#> GetoptLong 1.0.5 2020-12-15 [1] RSPM (R 4.3.0)
#> ggbeeswarm 0.7.2 2023-04-29 [1] RSPM (R 4.3.0)
#> ggplot2 * 3.4.2 2023-04-03 [1] RSPM (R 4.3.0)
#> ggrepel * 0.9.3 2023-02-03 [1] RSPM (R 4.3.0)
#> GlobalOptions 0.1.2 2020-06-10 [1] RSPM (R 4.3.0)
#> glue 1.6.2 2022-02-24 [2] RSPM (R 4.3.0)
#> golem 0.4.1 2023-06-05 [1] RSPM (R 4.3.0)
#> gplots 3.1.3 2022-04-25 [1] RSPM (R 4.3.0)
#> gridExtra 2.3 2017-09-09 [1] RSPM (R 4.3.0)
#> gtable 0.3.3 2023-03-21 [1] RSPM (R 4.3.0)
#> gtools 3.9.4 2022-11-27 [1] RSPM (R 4.3.0)
#> HDF5Array 1.28.1 2023-05-01 [1] Bioconductor
#> here * 1.0.1 2020-12-13 [1] RSPM (R 4.3.0)
#> highr 0.10 2022-12-22 [2] RSPM (R 4.3.0)
#> Hmisc * 5.1-0 2023-05-08 [1] RSPM (R 4.3.0)
#> hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0)
#> htmlTable 2.4.1 2022-07-07 [1] RSPM (R 4.3.0)
#> htmltools 0.5.5 2023-03-23 [2] RSPM (R 4.3.0)
#> htmlwidgets 1.6.2 2023-03-17 [2] RSPM (R 4.3.0)
#> httpuv 1.6.11 2023-05-11 [2] RSPM (R 4.3.0)
#> httr 1.4.6 2023-05-08 [2] RSPM (R 4.3.0)
#> igraph 1.5.0 2023-06-16 [1] RSPM (R 4.3.0)
#> interactiveDisplayBase 1.38.0 2023-04-25 [1] Bioconductor
#> IRanges * 2.34.1 2023-06-22 [1] Bioconductor
#> irlba 2.3.5.1 2022-10-03 [1] RSPM (R 4.3.0)
#> iSEE * 2.12.0 2023-04-25 [1] Bioconductor
#> iterators 1.0.14 2022-02-05 [1] RSPM (R 4.3.0)
#> jquerylib 0.1.4 2021-04-26 [2] RSPM (R 4.3.0)
#> jsonlite 1.8.7 2023-06-29 [2] RSPM (R 4.3.0)
#> KEGGREST 1.40.0 2023-04-25 [1] Bioconductor
#> KernSmooth 2.23-22 2023-07-10 [3] RSPM (R 4.3.0)
#> knitr 1.43 2023-05-25 [2] RSPM (R 4.3.0)
#> labeling 0.4.2 2020-10-20 [1] RSPM (R 4.3.0)
#> later 1.3.1 2023-05-02 [2] RSPM (R 4.3.0)
#> lattice 0.21-8 2023-04-05 [3] CRAN (R 4.3.0)
#> lazyeval 0.2.2 2019-03-15 [1] RSPM (R 4.3.0)
#> lifecycle 1.0.3 2022-10-07 [2] RSPM (R 4.3.0)
#> limma * 3.56.2 2023-06-04 [1] Bioconductor
#> lme4 1.1-34 2023-07-04 [1] RSPM (R 4.3.0)
#> lobstr * 1.1.2 2022-06-22 [1] RSPM (R 4.3.0)
#> locfit 1.5-9.8 2023-06-11 [1] RSPM (R 4.3.0)
#> lubridate 1.9.2 2023-02-10 [1] RSPM (R 4.3.0)
#> magick 2.7.4 2023-03-09 [1] RSPM (R 4.3.0)
#> magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.3.0)
#> maps 3.4.1 2022-10-30 [1] RSPM (R 4.3.0)
#> MASS 7.3-60 2023-05-04 [3] RSPM (R 4.3.0)
#> Matrix 1.6-0 2023-07-08 [3] RSPM (R 4.3.0)
#> MatrixGenerics * 1.12.2 2023-06-09 [1] Bioconductor
#> matrixStats * 1.0.0 2023-06-02 [1] RSPM (R 4.3.0)
#> memoise 2.0.1 2021-11-26 [2] RSPM (R 4.3.0)
#> mgcv 1.8-42 2023-03-02 [3] CRAN (R 4.3.0)
#> mime 0.12 2021-09-28 [2] RSPM (R 4.3.0)
#> miniUI 0.1.1.1 2018-05-18 [2] RSPM (R 4.3.0)
#> minqa 1.2.5 2022-10-19 [1] RSPM (R 4.3.0)
#> munsell 0.5.0 2018-06-12 [1] RSPM (R 4.3.0)
#> mvtnorm 1.2-2 2023-06-08 [1] RSPM (R 4.3.0)
#> nlme 3.1-162 2023-01-31 [3] CRAN (R 4.3.0)
#> nloptr 2.0.3 2022-05-26 [1] RSPM (R 4.3.0)
#> nnet 7.3-19 2023-05-03 [3] RSPM (R 4.3.0)
#> paletteer 1.5.0 2022-10-19 [1] RSPM (R 4.3.0)
#> patchwork * 1.1.2 2022-08-19 [1] RSPM (R 4.3.0)
#> pbkrtest 0.5.2 2023-01-19 [1] RSPM (R 4.3.0)
#> pheatmap * 1.0.12 2019-01-04 [1] RSPM (R 4.3.0)
#> pillar 1.9.0 2023-03-22 [2] RSPM (R 4.3.0)
#> pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.3.0)
#> plotly 4.10.2 2023-06-03 [1] RSPM (R 4.3.0)
#> plyr 1.8.8 2022-11-11 [1] RSPM (R 4.3.0)
#> png 0.1-8 2022-11-29 [1] RSPM (R 4.3.0)
#> Polychrome * 1.5.1 2022-05-03 [1] RSPM (R 4.3.0)
#> postcards * 0.2.3 2022-01-07 [1] RSPM (R 4.3.0)
#> prettyunits 1.1.1 2020-01-24 [2] RSPM (R 4.3.0)
#> progress 1.2.2 2019-05-16 [1] RSPM (R 4.3.0)
#> promises 1.2.0.1 2021-02-11 [2] RSPM (R 4.3.0)
#> purrr 1.0.1 2023-01-10 [2] RSPM (R 4.3.0)
#> R.cache 0.16.0 2022-07-21 [1] RSPM (R 4.3.0)
#> R.methodsS3 1.8.2 2022-06-13 [1] RSPM (R 4.3.0)
#> R.oo 1.25.0 2022-06-12 [1] RSPM (R 4.3.0)
#> R.utils 2.12.2 2022-11-11 [1] RSPM (R 4.3.0)
#> R6 2.5.1 2021-08-19 [2] RSPM (R 4.3.0)
#> rappdirs 0.3.3 2021-01-31 [2] RSPM (R 4.3.0)
#> rbibutils 2.2.13 2023-01-13 [1] RSPM (R 4.3.0)
#> RColorBrewer * 1.1-3 2022-04-03 [1] RSPM (R 4.3.0)
#> Rcpp 1.0.11 2023-07-06 [2] RSPM (R 4.3.0)
#> RCurl 1.98-1.12 2023-03-27 [1] RSPM (R 4.3.0)
#> Rdpack 2.4 2022-07-20 [1] RSPM (R 4.3.0)
#> recount3 * 1.10.2 2023-05-07 [1] Bioconductor
#> RefManageR * 1.4.0 2022-09-30 [1] RSPM (R 4.3.0)
#> remaCor 0.0.16 2023-06-21 [1] RSPM (R 4.3.0)
#> rematch2 2.1.2 2020-05-01 [2] RSPM (R 4.3.0)
#> reshape2 1.4.4 2020-04-09 [1] RSPM (R 4.3.0)
#> restfulr 0.0.15 2022-06-16 [1] RSPM (R 4.3.0)
#> rhdf5 2.44.0 2023-04-25 [1] Bioconductor
#> rhdf5filters 1.12.1 2023-04-30 [1] Bioconductor
#> Rhdf5lib 1.22.0 2023-04-25 [1] Bioconductor
#> RhpcBLASctl 0.23-42 2023-02-11 [1] RSPM (R 4.3.0)
#> rintrojs 0.3.2 2022-08-09 [1] RSPM (R 4.3.0)
#> rjson 0.2.21 2022-01-09 [1] RSPM (R 4.3.0)
#> rlang * 1.1.1 2023-04-28 [2] RSPM (R 4.3.0)
#> rmarkdown 2.23 2023-07-01 [2] RSPM (R 4.3.0)
#> rpart 4.1.19 2022-10-21 [3] CRAN (R 4.3.0)
#> rprojroot 2.0.3 2022-04-02 [2] RSPM (R 4.3.0)
#> Rsamtools 2.16.0 2023-04-25 [1] Bioconductor
#> RSQLite 2.3.1 2023-04-03 [1] RSPM (R 4.3.0)
#> rstudioapi 0.15.0 2023-07-07 [2] RSPM (R 4.3.0)
#> rsvd 1.0.5 2021-04-16 [1] RSPM (R 4.3.0)
#> rtracklayer 1.60.0 2023-04-25 [1] Bioconductor
#> S4Arrays 1.0.4 2023-05-14 [1] Bioconductor
#> S4Vectors * 0.38.1 2023-05-02 [1] Bioconductor
#> sass 0.4.6 2023-05-03 [2] RSPM (R 4.3.0)
#> ScaledMatrix 1.8.1 2023-05-03 [1] Bioconductor
#> scales 1.2.1 2022-08-20 [1] RSPM (R 4.3.0)
#> scater * 1.28.0 2023-04-25 [1] Bioconductor
#> scatterplot3d 0.3-44 2023-05-05 [1] RSPM (R 4.3.0)
#> scuttle * 1.10.1 2023-05-02 [1] Bioconductor
#> sessioninfo * 1.2.2 2021-12-06 [2] RSPM (R 4.3.0)
#> shape 1.4.6 2021-05-19 [1] RSPM (R 4.3.0)
#> shiny 1.7.4.1 2023-07-06 [2] RSPM (R 4.3.0)
#> shinyAce 0.4.2 2022-05-06 [1] RSPM (R 4.3.0)
#> shinydashboard 0.7.2 2021-09-30 [1] RSPM (R 4.3.0)
#> shinyjs 2.1.0 2021-12-23 [1] RSPM (R 4.3.0)
#> shinyWidgets 0.7.6 2023-01-08 [1] RSPM (R 4.3.0)
#> SingleCellExperiment * 1.22.0 2023-04-25 [1] Bioconductor
#> smokingMouse * 0.99.5 2023-06-28 [1] Github (LieberInstitute/smokingMouse@2e7640c)
#> spam 2.9-1 2022-08-07 [1] RSPM (R 4.3.0)
#> sparseMatrixStats 1.12.2 2023-07-02 [1] Bioconductor
#> SpatialExperiment * 1.10.0 2023-04-25 [1] Bioconductor
#> spatialLIBD * 1.12.0 2023-04-27 [1] Bioconductor
#> statmod 1.5.0 2023-01-06 [1] RSPM (R 4.3.0)
#> stringi 1.7.12 2023-01-11 [2] RSPM (R 4.3.0)
#> stringr * 1.5.0 2022-12-02 [2] RSPM (R 4.3.0)
#> styler 1.10.1 2023-06-05 [1] RSPM (R 4.3.0)
#> SummarizedExperiment * 1.30.2 2023-06-06 [1] Bioconductor
#> tibble 3.2.1 2023-03-20 [2] RSPM (R 4.3.0)
#> tidyr 1.3.0 2023-01-24 [1] RSPM (R 4.3.0)
#> tidyselect 1.2.0 2022-10-10 [1] RSPM (R 4.3.0)
#> timechange 0.2.0 2023-01-11 [1] RSPM (R 4.3.0)
#> usethis * 2.2.2 2023-07-06 [2] RSPM (R 4.3.0)
#> utf8 1.2.3 2023-01-31 [2] RSPM (R 4.3.0)
#> variancePartition * 1.30.2 2023-06-07 [1] Bioconductor
#> vctrs 0.6.3 2023-06-14 [2] RSPM (R 4.3.0)
#> vipor 0.4.5 2017-03-22 [1] RSPM (R 4.3.0)
#> viridis 0.6.3 2023-05-03 [1] RSPM (R 4.3.0)
#> viridisLite 0.4.2 2023-05-02 [1] RSPM (R 4.3.0)
#> withr 2.5.0 2022-03-03 [2] RSPM (R 4.3.0)
#> xfun 0.39 2023-04-20 [2] RSPM (R 4.3.0)
#> XML 3.99-0.14 2023-03-19 [1] RSPM (R 4.3.0)
#> xml2 1.3.5 2023-07-06 [2] RSPM (R 4.3.0)
#> xtable 1.8-4 2019-04-21 [2] RSPM (R 4.3.0)
#> XVector 0.40.0 2023-04-25 [1] Bioconductor
#> yaml 2.3.7 2023-01-23 [2] RSPM (R 4.3.0)
#> zlibbioc 1.46.0 2023-04-25 [1] Bioconductor
#>
#> [1] /__w/_temp/Library
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/local/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
This interactive book was last updated at 2023-07-11 23:16:25.702808.