Overview

Here you can find the files for the June 2024 Statistical Analysis of Genome Scale Data course at CSHL portion taught by Leo and his team (June 9-11).

Instructor:

Teaching assistants:

Download course materials

Download the materials for this course with usethis::use_course('lcolladotor/cshl_rstats_genome_scale_2024') or view online at lcolladotor.github.io/cshl_rstats_genome_scale_2024. This command downloads a static version of the course materials.

If you want to be able to easily download updates, we recommend using Git. Happy Git and GitHub for the useR is great for getting your computer ready to use Git and GitHub. If you already have a GitHub account, you can instead use this command to download the course:

## Download it the first time
git clone https://github.com/lcolladotor/cshl_rstats_genome_scale_2024.git

## To update the contents, use:
cd cshl_rstats_genome_scale_2024
git pull

Or you could use the GitHub Desktop application.

Code of Conduct

We’ll follow the CSHL code of conduct as well as version 1.2.0 of the Bioconductor code of conduct bioconductor.github.io/bioc_coc_multilingual/.

For reporting any violations of the code of conduct, report them to the Instructor and/or Course Coordinators.

Course Schedule

Local times in US Eastern

See CSHLData2024 for the detailed schedule.

Course Prerequisites

Install R 4.4.x from CRAN then install the following R packages:

## For installing Bioconductor packages
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

## Install required packages
BiocManager::install(
    c(
        "usethis", ## Utilities
        "BiocFileCache",
        "RefManageR",
        "gitcreds",
        "gert",
        "gh",
        "here",
        "Hmisc",
        "biocthis",
        "lobstr",
        "postcards",
        "scater",
        "sessioninfo",
        "stringr",
        "SummarizedExperiment", ## Main containers / vis
        "iSEE",
        "edgeR", ## RNA-seq
        "ExploreModelMatrix",
        "limma",
        "smokingMouse",
        "recount3",
        "rlang",
        "scRNAseq",
        "airway",
        "pheatmap", ## Visualization
        "ggplot2",
        "ggrepel",
        "patchwork",
        "RColorBrewer",
        "ComplexHeatmap",
        "cowplot",
        "Polychrome",
        "spatialLIBD", ## Advanced
        "variancePartition"
    )
)

You will also need to install RStudio version 2024.04.0+735 or newer.

R session information

Details on the R version used for making this book. The source code is available at lcolladotor/cshl_rstats_genome_scale_2024.

## Load the package at the top of your script
library("sessioninfo")

## Utilities
library("BiocFileCache")
library("BiocStyle")
library("biocthis")
library("gitcreds")
library("gert")
library("gh")
library("here")
library("lobstr")
library("postcards")
library("usethis")
library("sessioninfo")

## Data
library("smokingMouse")
library("scRNAseq")

## Main containers / vis
library("SummarizedExperiment")
library("iSEE")

## RNA-seq
library("airway")
library("edgeR")
library("ExploreModelMatrix")
library("limma")
library("recount3")

## QCA
library("scater")

## Variance Partition
library("variancePartition")

## Visualization: plots & text
library("ComplexHeatmap")
library("ggplot2")
library("patchwork")
library("pheatmap")
library("RColorBrewer")
library("Hmisc")
library("stringr")
library("cowplot")
library("rlang")
library("ggrepel")
library("Polychrome")

## Spatial transcriptomics
library("spatialLIBD")
## Reproducibility information
options(width = 120)
session_info()
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
##  setting  value
##  version  R version 4.4.0 (2024-04-24)
##  os       Ubuntu 22.04.4 LTS
##  system   x86_64, linux-gnu
##  ui       X11
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       UTC
##  date     2024-06-11
##  pandoc   3.1.13 @ /usr/bin/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
##  package              * version     date (UTC) lib source
##  abind                  1.4-5       2016-07-21 [1] RSPM (R 4.4.0)
##  airway               * 1.24.0      2024-05-02 [1] Bioconductor 3.19 (R 4.4.0)
##  alabaster.base         1.4.1       2024-05-03 [1] Bioconductor 3.19 (R 4.4.0)
##  alabaster.matrix       1.4.0       2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  alabaster.ranges       1.4.1       2024-05-21 [1] Bioconductor 3.19 (R 4.4.0)
##  alabaster.sce          1.4.0       2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  alabaster.schemas      1.4.0       2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  alabaster.se           1.4.1       2024-05-21 [1] Bioconductor 3.19 (R 4.4.0)
##  AnnotationDbi          1.66.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
##  AnnotationFilter       1.28.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  AnnotationHub          3.12.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
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##  askpass                1.2.0       2023-09-03 [2] RSPM (R 4.4.0)
##  attempt                0.3.1       2020-05-03 [1] RSPM (R 4.4.0)
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##  beeswarm               0.4.0       2021-06-01 [1] RSPM (R 4.4.0)
##  benchmarkme            1.0.8       2022-06-12 [1] RSPM (R 4.4.0)
##  benchmarkmeData        1.0.4       2020-04-23 [1] RSPM (R 4.4.0)
##  Biobase              * 2.64.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  BiocFileCache        * 2.12.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  BiocGenerics         * 0.50.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  BiocIO                 1.14.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  BiocManager            1.30.23     2024-05-04 [2] CRAN (R 4.4.0)
##  BiocNeighbors          1.22.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  BiocParallel         * 1.38.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  BiocSingular           1.20.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  BiocStyle            * 2.32.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  biocthis             * 1.14.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  BiocVersion            3.19.1      2024-04-17 [2] Bioconductor 3.19 (R 4.4.0)
##  Biostrings             2.72.1      2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
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##  bit64                  4.0.5       2020-08-30 [1] RSPM (R 4.4.0)
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##  blob                   1.2.4       2023-03-17 [1] RSPM (R 4.4.0)
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##  broom                  1.0.6       2024-05-17 [1] RSPM (R 4.4.0)
##  bslib                  0.7.0       2024-03-29 [2] RSPM (R 4.4.0)
##  cachem                 1.1.0       2024-05-16 [2] RSPM (R 4.4.0)
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##  circlize               0.4.16      2024-02-20 [1] RSPM (R 4.4.0)
##  cli                    3.6.2       2023-12-11 [2] RSPM (R 4.4.0)
##  clue                   0.3-65      2023-09-23 [1] RSPM (R 4.4.0)
##  cluster                2.1.6       2023-12-01 [3] CRAN (R 4.4.0)
##  codetools              0.2-20      2024-03-31 [3] CRAN (R 4.4.0)
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##  colourpicker           1.3.0       2023-08-21 [1] RSPM (R 4.4.0)
##  ComplexHeatmap       * 2.20.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  config                 0.3.2       2023-08-30 [1] RSPM (R 4.4.0)
##  corpcor                1.6.10      2021-09-16 [1] RSPM (R 4.4.0)
##  cowplot              * 1.1.3       2024-01-22 [1] RSPM (R 4.4.0)
##  crayon                 1.5.2       2022-09-29 [2] RSPM (R 4.4.0)
##  credentials            2.0.1       2023-09-06 [2] RSPM (R 4.4.0)
##  curl                   5.2.1       2024-03-01 [1] RSPM (R 4.4.0)
##  data.table             1.15.4      2024-03-30 [1] RSPM (R 4.4.0)
##  DBI                    1.2.3       2024-06-02 [1] RSPM (R 4.4.0)
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##  DelayedMatrixStats     1.26.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  digest                 0.6.35      2024-03-11 [2] RSPM (R 4.4.0)
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##  dotCall64              1.1-1       2023-11-28 [1] RSPM (R 4.4.0)
##  dplyr                  1.1.4       2023-11-17 [1] RSPM (R 4.4.0)
##  DT                     0.33        2024-04-04 [1] RSPM (R 4.4.0)
##  edgeR                * 4.2.0       2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  ensembldb              2.28.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  EnvStats               2.8.1       2023-08-22 [1] RSPM (R 4.4.0)
##  evaluate               0.24.0      2024-06-10 [2] RSPM (R 4.4.0)
##  ExperimentHub          2.12.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  ExploreModelMatrix   * 1.16.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  fANCOVA                0.6-1       2020-11-13 [1] RSPM (R 4.4.0)
##  fansi                  1.0.6       2023-12-08 [2] RSPM (R 4.4.0)
##  fastmap                1.2.0       2024-05-15 [2] RSPM (R 4.4.0)
##  fields                 15.2        2023-08-17 [1] RSPM (R 4.4.0)
##  filelock               1.0.3       2023-12-11 [1] RSPM (R 4.4.0)
##  foreach                1.5.2       2022-02-02 [1] RSPM (R 4.4.0)
##  foreign                0.8-86      2023-11-28 [3] CRAN (R 4.4.0)
##  Formula                1.2-5       2023-02-24 [1] RSPM (R 4.4.0)
##  fs                     1.6.4       2024-04-25 [2] RSPM (R 4.4.0)
##  generics               0.1.3       2022-07-05 [1] RSPM (R 4.4.0)
##  GenomeInfoDb         * 1.40.1      2024-05-24 [1] Bioconductor 3.19 (R 4.4.0)
##  GenomeInfoDbData       1.2.12      2024-05-26 [1] Bioconductor
##  GenomicAlignments      1.40.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  GenomicFeatures        1.56.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  GenomicRanges        * 1.56.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
##  gert                 * 2.0.1       2023-12-04 [2] RSPM (R 4.4.0)
##  GetoptLong             1.0.5       2020-12-15 [1] RSPM (R 4.4.0)
##  ggbeeswarm             0.7.2       2023-04-29 [1] RSPM (R 4.4.0)
##  ggplot2              * 3.5.1       2024-04-23 [1] RSPM (R 4.4.0)
##  ggrepel              * 0.9.5       2024-01-10 [1] RSPM (R 4.4.0)
##  gh                   * 1.4.1       2024-03-28 [2] RSPM (R 4.4.0)
##  gitcreds             * 0.1.2       2022-09-08 [2] RSPM (R 4.4.0)
##  GlobalOptions          0.1.2       2020-06-10 [1] RSPM (R 4.4.0)
##  glue                   1.7.0       2024-01-09 [2] RSPM (R 4.4.0)
##  golem                  0.4.1       2023-06-05 [1] RSPM (R 4.4.0)
##  gplots                 3.1.3.1     2024-02-02 [1] RSPM (R 4.4.0)
##  gridExtra              2.3         2017-09-09 [1] RSPM (R 4.4.0)
##  gtable                 0.3.5       2024-04-22 [1] RSPM (R 4.4.0)
##  gtools                 3.9.5       2023-11-20 [1] RSPM (R 4.4.0)
##  gypsum                 1.0.1       2024-05-08 [1] Bioconductor 3.19 (R 4.4.0)
##  HDF5Array              1.32.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  here                 * 1.0.1       2020-12-13 [1] RSPM (R 4.4.0)
##  Hmisc                * 5.1-3       2024-05-28 [1] RSPM (R 4.4.0)
##  htmlTable              2.4.2       2023-10-29 [1] RSPM (R 4.4.0)
##  htmltools              0.5.8.1     2024-04-04 [2] RSPM (R 4.4.0)
##  htmlwidgets            1.6.4       2023-12-06 [2] RSPM (R 4.4.0)
##  httpuv                 1.6.15      2024-03-26 [2] RSPM (R 4.4.0)
##  httr                   1.4.7       2023-08-15 [2] RSPM (R 4.4.0)
##  httr2                  1.0.1       2024-04-01 [2] RSPM (R 4.4.0)
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##  irlba                  2.3.5.1     2022-10-03 [1] RSPM (R 4.4.0)
##  iSEE                 * 2.16.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
##  iterators              1.0.14      2022-02-05 [1] RSPM (R 4.4.0)
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##  jsonlite               1.8.8       2023-12-04 [2] RSPM (R 4.4.0)
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##  knitr                  1.47        2024-05-29 [2] RSPM (R 4.4.0)
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##  lazyeval               0.2.2       2019-03-15 [1] RSPM (R 4.4.0)
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##  lmerTest               3.1-3       2020-10-23 [1] RSPM (R 4.4.0)
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##  S4Arrays               1.4.1       2024-05-20 [1] Bioconductor 3.19 (R 4.4.0)
##  S4Vectors            * 0.42.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  sass                   0.4.9       2024-03-15 [2] RSPM (R 4.4.0)
##  ScaledMatrix           1.12.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  scales                 1.3.0       2023-11-28 [1] RSPM (R 4.4.0)
##  scater               * 1.32.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  scatterplot3d          0.3-44      2023-05-05 [1] RSPM (R 4.4.0)
##  scRNAseq             * 2.18.0      2024-05-02 [1] Bioconductor 3.19 (R 4.4.0)
##  scuttle              * 1.14.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  sessioninfo          * 1.2.2       2021-12-06 [2] RSPM (R 4.4.0)
##  shape                  1.4.6.1     2024-02-23 [1] RSPM (R 4.4.0)
##  shiny                  1.8.1.1     2024-04-02 [2] RSPM (R 4.4.0)
##  shinyAce               0.4.2       2022-05-06 [1] RSPM (R 4.4.0)
##  shinydashboard         0.7.2       2021-09-30 [1] RSPM (R 4.4.0)
##  shinyjs                2.1.0       2021-12-23 [1] RSPM (R 4.4.0)
##  shinyWidgets           0.8.6       2024-04-24 [1] RSPM (R 4.4.0)
##  SingleCellExperiment * 1.26.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  smokingMouse         * 0.99.91     2024-06-11 [1] Github (LieberInstitute/smokingMouse@96d8480)
##  spam                   2.10-0      2023-10-23 [1] RSPM (R 4.4.0)
##  SparseArray            1.4.8       2024-05-24 [1] Bioconductor 3.19 (R 4.4.0)
##  sparseMatrixStats      1.16.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  SpatialExperiment    * 1.14.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
##  spatialLIBD          * 1.16.2      2024-05-28 [1] Bioconductor 3.19 (R 4.4.0)
##  statmod                1.5.0       2023-01-06 [1] RSPM (R 4.4.0)
##  stringi                1.8.4       2024-05-06 [2] RSPM (R 4.4.0)
##  stringr              * 1.5.1       2023-11-14 [2] RSPM (R 4.4.0)
##  styler                 1.10.3      2024-04-07 [1] RSPM (R 4.4.0)
##  SummarizedExperiment * 1.34.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
##  sys                    3.4.2       2023-05-23 [2] RSPM (R 4.4.0)
##  tibble                 3.2.1       2023-03-20 [2] RSPM (R 4.4.0)
##  tidyr                  1.3.1       2024-01-24 [1] RSPM (R 4.4.0)
##  tidyselect             1.2.1       2024-03-11 [1] RSPM (R 4.4.0)
##  UCSC.utils             1.0.0       2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  usethis              * 2.2.3       2024-02-19 [2] RSPM (R 4.4.0)
##  utf8                   1.2.4       2023-10-22 [2] RSPM (R 4.4.0)
##  variancePartition    * 1.34.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  vctrs                  0.6.5       2023-12-01 [2] RSPM (R 4.4.0)
##  vipor                  0.4.7       2023-12-18 [1] RSPM (R 4.4.0)
##  viridis                0.6.5       2024-01-29 [1] RSPM (R 4.4.0)
##  viridisLite            0.4.2       2023-05-02 [1] RSPM (R 4.4.0)
##  withr                  3.0.0       2024-01-16 [2] RSPM (R 4.4.0)
##  xfun                   0.44        2024-05-15 [2] RSPM (R 4.4.0)
##  XML                    3.99-0.16.1 2024-01-22 [1] RSPM (R 4.4.0)
##  xtable                 1.8-4       2019-04-21 [2] RSPM (R 4.4.0)
##  XVector                0.44.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
##  yaml                   2.3.8       2023-12-11 [2] RSPM (R 4.4.0)
##  zlibbioc               1.50.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
## 
##  [1] /__w/_temp/Library
##  [2] /usr/local/lib/R/site-library
##  [3] /usr/local/lib/R/library
## 
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
proc.time()
##    user  system elapsed 
##  14.164   1.086  15.047

System curl version:

curl::curl_version()
## $version
## [1] "7.81.0"
## 
## $ssl_version
## [1] "OpenSSL/3.0.2"
## 
## $libz_version
## [1] "1.2.11"
## 
## $libssh_version
## [1] "libssh/0.9.6/openssl/zlib"
## 
## $libidn_version
## [1] "2.3.2"
## 
## $host
## [1] "x86_64-pc-linux-gnu"
## 
## $protocols
##  [1] "dict"    "file"    "ftp"     "ftps"    "gopher"  "gophers" "http"    "https"   "imap"    "imaps"   "ldap"   
## [12] "ldaps"   "mqtt"    "pop3"    "pop3s"   "rtmp"    "rtsp"    "scp"     "sftp"    "smb"     "smbs"    "smtp"   
## [23] "smtps"   "telnet"  "tftp"   
## 
## $ipv6
## [1] TRUE
## 
## $http2
## [1] TRUE
## 
## $idn
## [1] TRUE

This interactive book was last updated at 2024-06-11 19:59:57.396482.

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

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