Statistical Analysis of Genome Scale Data 2023
Overview
Here you can find the files for the July 2023 Statistical Analysis of Genome Scale Data course at CSHL portion taught by Leo and his team (July 3rd to July 6th). See CSHLData2023 for a list of all instructors and related materials.
Instructor:
Teach assistants:
Happy to welcome @lcolladotor, @SubmarineGene, and @daianna_glez to @cshlcourses on Statistical Analysis of Genome Scale Data. Materials here:https://t.co/0JGzEEf3Yx
— Sean Davis (@seandavis12) July 3, 2023
Interested in learning R/@Bioconductor for #RNAseq data analysis?
— 🇲🇽 Leonardo Collado-Torres (@lcolladotor) July 10, 2023
Check https://t.co/jcNWOq7VWD that @daianna_glez @SubmarineGene and I built for a CSHL course organized by @seandavis12 & Vincent Carey#rstats @LieberInstitute @cshlcourses
Source at https://t.co/aQ8kLMadSl ⭐️
Download course materials
Download the materials for this course with usethis::use_course('lcolladotor/cshl_rstats_genome_scale_2023') or view online at lcolladotor.github.io/cshl_rstats_genome_scale_2023. 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_2023.git
## To update the contents, use:
cd cshl_rstats_genome_scale_2023
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 Schedule
Local times in US Eastern
See CSHLData2023 for the detailed schedule. Below is a list of the key packages we will use each day:
- Monday July 3rd:
SummarizedExperiment,iSEE,smokingMouse,biocthis - Tuesday July 4th:
recount3,ExploreModelMatrix,limma - Wednesday July 5th:
variancePartition,ComplexHeatmap - Thursday July 6th:
spatialLIBD
External links
- CSHL course
- CSHLData2023
- GitHub source code
- Slack
- Example real project (by Daianna): LieberInstitute/smokingMouse_Indirects
SPEAQeasyWorkshop2023for BioC2023 (by Daianna and Renee): LieberInstitute/SPEAQeasyWorkshop2023- LieberInstitute/template_project
- LIBD rstats club: check the public schedule
Course Prerequisites
Install R 4.3.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",
"here",
"Hmisc",
"biocthis",
"lobstr",
"postcards",
"scater",
"sessioninfo",
"smokingMouse",
"stringr",
"SummarizedExperiment", ## Main containers / vis
"iSEE",
"edgeR", ## RNA-seq
"ExploreModelMatrix",
"limma",
"recount3",
"rlang",
"pheatmap", ## Visualization
"ggplot2",
"ggrepel",
"patchwork",
"RColorBrewer",
"ComplexHeatmap",
"cowplot",
"Polychrome",
"spatialLIBD", ## Advanced
"variancePartition"
)
)
## Install smokingMouse, which is currently under review at Bioconductor
## at https://github.com/Bioconductor/Contributions/issues/3024.
BiocManager::install("LieberInstitute/smokingMouse")
## Required to access some recent bug fixes on biocthis
BiocManager::install("lcolladotor/biocthis")You will also need to install RStudio version 2023.06.0+421 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_2023.
## Load the package at the top of your script
library("sessioninfo")
## Utilities
library("BiocFileCache")
library("BiocStyle")
library("biocthis")
library("here")
library("lobstr")
library("postcards")
library("usethis")
library("sessioninfo")
## Data
library("smokingMouse")
## Main containers / vis
library("SummarizedExperiment")
library("iSEE")
## RNA-seq
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 4.3.0 (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
## 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)
## 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)
## 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)
## 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)
## 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)
## 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)
## 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
## 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)
## 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)
## 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
##
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────proc.time()## user system elapsed
## 22.241 1.137 23.408This interactive book was last updated at 2023-07-11 22:06:42.77207.
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