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
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#>  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)
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#>  Rsamtools                2.16.0    2023-04-25 [1] Bioconductor
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#>  rtracklayer              1.60.0    2023-04-25 [1] Bioconductor
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#>  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)
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#>  smokingMouse           * 0.99.5    2023-06-28 [1] Github (LieberInstitute/smokingMouse@2e7640c)
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#>  sparseMatrixStats        1.12.2    2023-07-02 [1] Bioconductor
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#>  stringr                * 1.5.0     2022-12-02 [2] RSPM (R 4.3.0)
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#>  timechange               0.2.0     2023-01-11 [1] RSPM (R 4.3.0)
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#>  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.

© 2011-2023. All thoughts and opinions here are my own. The icon was designed by Mauricio Guzmán and is inspired by Huichol culture; it represents my community building interests.

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