Statistical Analysis of Genome Scale Data 2024
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:
Thanks again Sean Davis for inviting us to help teach https://t.co/KulvuQ3XK8 at @cshlcourses!
— 🇲🇽 Leonardo Collado-Torres (@lcolladotor) June 9, 2024
Our teaching materials are available at https://t.co/OP2YYZmqwh 📚
It’s an honor to teach with @lcgunam students & remote @LieberInstitute team members#rstats @Bioconductor pic.twitter.com/U4DzQuPvIn
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 pullOr 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 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")## ─ 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)
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## 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)
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## alabaster.se 1.4.1 2024-05-21 [1] Bioconductor 3.19 (R 4.4.0)
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## 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)
## aod 1.3.3 2023-12-13 [1] RSPM (R 4.4.0)
## askpass 1.2.0 2023-09-03 [2] RSPM (R 4.4.0)
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## benchmarkmeData 1.0.4 2020-04-23 [1] RSPM (R 4.4.0)
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## 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)
## bit 4.0.5 2022-11-15 [1] RSPM (R 4.4.0)
## bit64 4.0.5 2020-08-30 [1] RSPM (R 4.4.0)
## bitops 1.0-7 2021-04-24 [1] RSPM (R 4.4.0)
## blob 1.2.4 2023-03-17 [1] RSPM (R 4.4.0)
## bookdown 0.39 2024-04-15 [1] RSPM (R 4.4.0)
## boot 1.3-30 2024-02-26 [3] CRAN (R 4.4.0)
## 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)
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## caTools 1.18.2 2021-03-28 [1] RSPM (R 4.4.0)
## checkmate 2.3.1 2023-12-04 [1] RSPM (R 4.4.0)
## 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)
## colorspace 2.1-0 2023-01-23 [1] RSPM (R 4.4.0)
## 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)
## dbplyr * 2.5.0 2024-03-19 [1] RSPM (R 4.4.0)
## DelayedArray 0.30.1 2024-05-07 [1] Bioconductor 3.19 (R 4.4.0)
## 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)
## doParallel 1.0.17 2022-02-07 [1] RSPM (R 4.4.0)
## 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)
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## httr 1.4.7 2023-08-15 [2] RSPM (R 4.4.0)
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## igraph 2.0.3 2024-03-13 [1] RSPM (R 4.4.0)
## IRanges * 2.38.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
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## 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)
## jquerylib 0.1.4 2021-04-26 [2] RSPM (R 4.4.0)
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## magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.4.0)
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## MASS 7.3-60.2 2024-05-06 [3] local
## Matrix 1.7-0 2024-03-22 [3] CRAN (R 4.4.0)
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## memoise 2.0.1 2021-11-26 [2] RSPM (R 4.4.0)
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## Polychrome * 1.5.1 2022-05-03 [1] RSPM (R 4.4.0)
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## 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)
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## smokingMouse * 0.99.91 2024-06-11 [1] Github (LieberInstitute/smokingMouse@96d8480)
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## 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
##
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────## user system elapsed
## 14.164 1.086 15.047System 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] TRUEThis interactive book was last updated at 2024-06-11 19:59:57.396482.
License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.