Intro RNA-seq LCG-UNAM 2023
Overview
Here you can find the files for the February 2023 introduction to R, RStudio and RNA-sequencing (RNA-seq) course for LCG-UNAM at CCG-UNAM (January 31 - February 3, 2023). The rest of the chapters will be in Spanish.
Instructor:
Teach assistants:
Guest presenters:
Course Coordinators:
- Heladia Salgado
- Julio Collado Vides
Download the materials for this course with usethis::use_course('lcolladotor/rnaseq_LCG-UNAM_2023') or view online at lcolladotor.github.io/rnaseq_LCG-UNAM_2023.
Code of Conduct
We’ll follow the CDSB code of conduct comunidadbioinfo.github.io/codigo-de-conducta/ 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 Cuernavaca, Mexico
- Tuesday January 31:
- Wednesday February 1:
- 9-11 am: expression data R/Bioconductor objects and visualization: SummarizedExperiment and iSEE
- 12-2 pm: Downloading RNA-seq data using recount3
- Thursday February 2:
- 9-11 am: statistical models with ExploreModelMatrix
- 11 am-12 pm + 1-2 pm: differential expression analysis with limma
- Friday February 3:
- 9-11 am: LieberInstitute/smokingMouse_Indirects results + code by Daianna González Padilla. Looking beyond this course!
- 12-12:30 pm:
pheatmapexercise solutions review - 12:30-2:30 pm: review + R/Bioconductor-powered Team Data Science overview
- 2:30-3 pm: open discussion (career paths, networking, etc)
- 2023 LIBD summer internship program: application closes 2/15.
External links
- Cursos LCG
- GitHub source code
- Zoom (ask)
- LCG-UNAM RStudio server
- CDSB.
- Slack CDSB Mexico, in particular the
intro_rnaseq_lcg_2023channel. You can join this Slack workspace through this link. - LieberInstitute/template_project
- Example real project (by Daianna): LieberInstitute/smokingMouse_Indirects
Course Prerequisites
Install R 4.2.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
"here",
"biocthis",
"lobstr",
"postcards",
"sessioninfo",
"SummarizedExperiment", ## Main containers / vis
"iSEE",
"edgeR", ## RNA-seq
"ExploreModelMatrix",
"limma",
"recount3",
"pheatmap", ## Visualization
"ggplot2",
"patchwork",
"RColorBrewer",
"ComplexHeatmap",
"spatialLIBD" ## Advanced
)
)You will also need to install RStudio version 2022.12.0+353 or newer.
Course Evaluation
- Participation
- (main evidence) written and/or verbal participation during class
- (optional, strongly encouraged for your own career) Community building: CDSB Slack (introduce yourself), Twitter, GitHub, etc.
- Public work
- (main evidence) Taking notes on GitHub
- (optional) Deploy an iSEE
shinyapp on shinyapps.io - (advanced and optional) R package with notes following
usethis::create_package()+biocthis::use_bioc_pkg_templates().
- Final project
- (main evidence) code in a public GitHub repository (different from the notes one) following the structure from LieberInstitute/template_project
- (optional) a rendered Rmd file (RPubs, GitHub, etc) on a public URL
- (optional advanced) Copy this repository, remove all the Rmds except the index.Rmd and edit accordingly. GitHub Actions will then help you render it. You’ll need to fetch the
gh-pagesbranch and at least make one commit for the HTML to be available such as this commit. You might also run into this GitHub default permission setting that you’ll need to change.
The final grade will be a weighted average from the evaluation by the TA (20%), your public work (40%) and your final project (40%).
Projects, public work and notes are due at 9 am US Eastern on Monday February 13th, though we recommend doing any work related to this course by Friday February 10th.
R session information
Details on the R version used for making this book. The source code is available at lcolladotor/rnaseq_LCG-UNAM_2023.
## Load the package at the top of your script
library("sessioninfo")
## Utilities
library("BiocStyle")
library("biocthis")
library("here")
library("lobstr")
library("postcards")
library("usethis")
library("sessioninfo")
## Main containers / vis
library("SummarizedExperiment")
library("iSEE")
## RNA-seq
library("edgeR")
library("ExploreModelMatrix")
library("limma")
library("recount3")
## Visualization
library("ComplexHeatmap")
library("ggplot2")
library("patchwork")
library("pheatmap")
library("RColorBrewer")
## Advanced
library("spatialLIBD")## Reproducibility information
options(width = 120)
session_info()## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.2 (2022-10-31)
## os Ubuntu 22.04.1 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz UTC
## date 2023-02-03
## pandoc 2.19.2 @ /usr/local/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## AnnotationDbi 1.60.0 2022-11-01 [1] Bioconductor
## AnnotationHub 3.6.0 2022-11-01 [1] Bioconductor
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.2)
## attempt 0.3.1 2020-05-03 [1] CRAN (R 4.2.2)
## beachmat 2.14.0 2022-11-01 [1] Bioconductor
## beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.2.2)
## benchmarkme 1.0.8 2022-06-12 [1] CRAN (R 4.2.2)
## benchmarkmeData 1.0.4 2020-04-23 [1] CRAN (R 4.2.2)
## Biobase * 2.58.0 2022-11-01 [1] Bioconductor
## BiocFileCache 2.6.0 2022-11-01 [1] Bioconductor
## BiocGenerics * 0.44.0 2022-11-01 [1] Bioconductor
## BiocIO 1.8.0 2022-11-01 [1] Bioconductor
## BiocManager 1.30.19 2022-10-25 [2] CRAN (R 4.2.2)
## BiocNeighbors 1.16.0 2022-11-01 [1] Bioconductor
## BiocParallel 1.32.5 2022-12-23 [1] Bioconductor
## BiocSingular 1.14.0 2022-11-01 [1] Bioconductor
## BiocStyle * 2.26.0 2022-11-01 [1] Bioconductor
## biocthis * 1.8.1 2022-11-02 [1] Bioconductor
## BiocVersion 3.16.0 2022-04-26 [2] Bioconductor
## Biostrings 2.66.0 2022-11-01 [1] Bioconductor
## bit 4.0.5 2022-11-15 [1] CRAN (R 4.2.2)
## bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.2)
## bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.2)
## blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.2)
## bookdown 0.32 2023-01-17 [1] RSPM (R 4.2.0)
## bslib 0.4.2 2022-12-16 [2] RSPM (R 4.2.0)
## cachem 1.0.6 2021-08-19 [2] RSPM (R 4.2.0)
## circlize 0.4.15 2022-05-10 [1] CRAN (R 4.2.2)
## cli 3.6.0 2023-01-09 [2] RSPM (R 4.2.0)
## clue 0.3-64 2023-01-31 [1] RSPM (R 4.2.0)
## cluster 2.1.4 2022-08-22 [3] CRAN (R 4.2.2)
## codetools 0.2-19 2023-02-01 [3] RSPM (R 4.2.0)
## colorspace 2.1-0 2023-01-23 [1] RSPM (R 4.2.0)
## colourpicker 1.2.0 2022-10-28 [1] CRAN (R 4.2.2)
## ComplexHeatmap * 2.14.0 2022-11-01 [1] Bioconductor
## config 0.3.1 2020-12-17 [1] CRAN (R 4.2.2)
## cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.2.2)
## crayon 1.5.2 2022-09-29 [2] RSPM (R 4.2.0)
## curl 5.0.0 2023-01-12 [2] RSPM (R 4.2.0)
## data.table 1.14.6 2022-11-16 [1] CRAN (R 4.2.2)
## DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.2)
## dbplyr 2.3.0 2023-01-16 [1] RSPM (R 4.2.0)
## DelayedArray 0.24.0 2022-11-01 [1] Bioconductor
## DelayedMatrixStats 1.20.0 2022-11-01 [1] Bioconductor
## desc 1.4.2 2022-09-08 [2] RSPM (R 4.2.0)
## digest 0.6.31 2022-12-11 [2] RSPM (R 4.2.0)
## doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.2.2)
## dotCall64 1.0-2 2022-10-03 [1] CRAN (R 4.2.2)
## dplyr 1.1.0 2023-01-29 [1] RSPM (R 4.2.0)
## dqrng 0.3.0 2021-05-01 [1] CRAN (R 4.2.2)
## DropletUtils 1.18.1 2022-11-22 [1] Bioconductor
## DT 0.27 2023-01-17 [1] RSPM (R 4.2.0)
## edgeR * 3.40.2 2023-01-19 [1] Bioconductor
## ellipsis 0.3.2 2021-04-29 [2] RSPM (R 4.2.0)
## evaluate 0.20 2023-01-17 [2] RSPM (R 4.2.0)
## ExperimentHub 2.6.0 2022-11-01 [1] Bioconductor
## ExploreModelMatrix * 1.10.0 2022-11-01 [1] Bioconductor
## fansi 1.0.4 2023-01-22 [2] RSPM (R 4.2.0)
## fastmap 1.1.0 2021-01-25 [2] RSPM (R 4.2.0)
## fields 14.1 2022-08-12 [1] CRAN (R 4.2.2)
## filelock 1.0.2 2018-10-05 [1] CRAN (R 4.2.2)
## foreach 1.5.2 2022-02-02 [1] CRAN (R 4.2.2)
## fs 1.6.0 2023-01-23 [2] RSPM (R 4.2.0)
## generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.2)
## GenomeInfoDb * 1.34.8 2023-02-01 [1] Bioconductor
## GenomeInfoDbData 1.2.9 2022-12-06 [1] Bioconductor
## GenomicAlignments 1.34.0 2022-11-01 [1] Bioconductor
## GenomicRanges * 1.50.2 2022-12-16 [1] Bioconductor
## GetoptLong 1.0.5 2020-12-15 [1] CRAN (R 4.2.2)
## ggbeeswarm 0.7.1 2022-12-16 [1] RSPM (R 4.2.0)
## ggplot2 * 3.4.0 2022-11-04 [1] CRAN (R 4.2.2)
## ggrepel 0.9.2 2022-11-06 [1] CRAN (R 4.2.2)
## GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.2.2)
## glue 1.6.2 2022-02-24 [2] RSPM (R 4.2.0)
## golem 0.3.5 2022-10-18 [1] CRAN (R 4.2.2)
## gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.2)
## gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.2)
## HDF5Array 1.26.0 2022-11-01 [1] Bioconductor
## here * 1.0.1 2020-12-13 [1] CRAN (R 4.2.2)
## htmltools 0.5.4 2022-12-07 [2] RSPM (R 4.2.0)
## htmlwidgets 1.6.1 2023-01-07 [2] RSPM (R 4.2.0)
## httpuv 1.6.8 2023-01-12 [2] RSPM (R 4.2.0)
## httr 1.4.4 2022-08-17 [2] RSPM (R 4.2.0)
## igraph 1.3.5 2022-09-22 [1] CRAN (R 4.2.2)
## interactiveDisplayBase 1.36.0 2022-11-01 [1] Bioconductor
## IRanges * 2.32.0 2022-11-01 [1] Bioconductor
## irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.2.2)
## iSEE * 2.10.0 2022-11-01 [1] Bioconductor
## iterators 1.0.14 2022-02-05 [1] CRAN (R 4.2.2)
## jquerylib 0.1.4 2021-04-26 [2] RSPM (R 4.2.0)
## jsonlite 1.8.4 2022-12-06 [2] RSPM (R 4.2.0)
## KEGGREST 1.38.0 2022-11-01 [1] Bioconductor
## knitr 1.42 2023-01-25 [2] RSPM (R 4.2.0)
## later 1.3.0 2021-08-18 [2] RSPM (R 4.2.0)
## lattice 0.20-45 2021-09-22 [3] CRAN (R 4.2.2)
## lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.2.2)
## lifecycle 1.0.3 2022-10-07 [2] RSPM (R 4.2.0)
## limma * 3.54.1 2023-01-26 [1] Bioconductor
## lobstr * 1.1.2 2022-06-22 [1] CRAN (R 4.2.2)
## locfit 1.5-9.7 2023-01-02 [1] RSPM (R 4.2.0)
## magick 2.7.3 2021-08-18 [1] CRAN (R 4.2.2)
## magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.2.0)
## maps 3.4.1 2022-10-30 [1] CRAN (R 4.2.2)
## MASS 7.3-58.2 2023-01-23 [3] RSPM (R 4.2.0)
## Matrix 1.5-3 2022-11-11 [3] RSPM (R 4.2.0)
## MatrixGenerics * 1.10.0 2022-11-01 [1] Bioconductor
## matrixStats * 0.63.0 2022-11-18 [1] CRAN (R 4.2.2)
## memoise 2.0.1 2021-11-26 [2] RSPM (R 4.2.0)
## mgcv 1.8-41 2022-10-21 [3] CRAN (R 4.2.2)
## mime 0.12 2021-09-28 [2] RSPM (R 4.2.0)
## miniUI 0.1.1.1 2018-05-18 [2] RSPM (R 4.2.0)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.2)
## nlme 3.1-162 2023-01-31 [3] RSPM (R 4.2.0)
## paletteer 1.5.0 2022-10-19 [1] RSPM (R 4.2.0)
## patchwork * 1.1.2 2022-08-19 [1] CRAN (R 4.2.2)
## pheatmap * 1.0.12 2019-01-04 [1] CRAN (R 4.2.2)
## pillar 1.8.1 2022-08-19 [2] RSPM (R 4.2.0)
## pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.2.0)
## pkgload 1.3.2 2022-11-16 [2] RSPM (R 4.2.0)
## plotly 4.10.1 2022-11-07 [1] CRAN (R 4.2.2)
## png 0.1-8 2022-11-29 [1] CRAN (R 4.2.2)
## postcards * 0.2.3 2022-01-07 [1] RSPM (R 4.2.0)
## promises 1.2.0.1 2021-02-11 [2] RSPM (R 4.2.0)
## purrr 1.0.1 2023-01-10 [2] RSPM (R 4.2.0)
## R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.2)
## R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.2)
## R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.2)
## R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.2.2)
## R6 2.5.1 2021-08-19 [2] RSPM (R 4.2.0)
## rappdirs 0.3.3 2021-01-31 [2] RSPM (R 4.2.0)
## RColorBrewer * 1.1-3 2022-04-03 [1] CRAN (R 4.2.2)
## Rcpp 1.0.10 2023-01-22 [2] RSPM (R 4.2.0)
## RCurl 1.98-1.10 2023-01-27 [1] RSPM (R 4.2.0)
## recount3 * 1.8.0 2022-11-01 [1] Bioconductor
## rematch2 2.1.2 2020-05-01 [2] RSPM (R 4.2.0)
## restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.2.2)
## rhdf5 2.42.0 2022-11-01 [1] Bioconductor
## rhdf5filters 1.10.0 2022-11-01 [1] Bioconductor
## Rhdf5lib 1.20.0 2022-11-01 [1] Bioconductor
## rintrojs 0.3.2 2022-08-09 [1] CRAN (R 4.2.2)
## rjson 0.2.21 2022-01-09 [1] CRAN (R 4.2.2)
## rlang 1.0.6 2022-09-24 [2] RSPM (R 4.2.0)
## rmarkdown 2.20 2023-01-19 [2] RSPM (R 4.2.0)
## roxygen2 7.2.3 2022-12-08 [2] RSPM (R 4.2.0)
## rprojroot 2.0.3 2022-04-02 [2] RSPM (R 4.2.0)
## Rsamtools 2.14.0 2022-11-01 [1] Bioconductor
## RSQLite 2.2.20 2022-12-22 [1] RSPM (R 4.2.0)
## rstudioapi 0.14 2022-08-22 [2] RSPM (R 4.2.0)
## rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.2.2)
## rtracklayer 1.58.0 2022-11-01 [1] Bioconductor
## S4Vectors * 0.36.1 2022-12-05 [1] Bioconductor
## sass 0.4.5 2023-01-24 [2] RSPM (R 4.2.0)
## ScaledMatrix 1.6.0 2022-11-01 [1] Bioconductor
## scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.2)
## scater 1.26.1 2022-11-13 [1] Bioconductor
## scuttle 1.8.4 2023-01-19 [1] Bioconductor
## sessioninfo * 1.2.2 2021-12-06 [2] RSPM (R 4.2.0)
## shape 1.4.6 2021-05-19 [1] CRAN (R 4.2.2)
## shiny 1.7.4 2022-12-15 [2] RSPM (R 4.2.0)
## shinyAce 0.4.2 2022-05-06 [1] CRAN (R 4.2.2)
## shinydashboard 0.7.2 2021-09-30 [1] CRAN (R 4.2.2)
## shinyjs 2.1.0 2021-12-23 [1] CRAN (R 4.2.2)
## shinyWidgets 0.7.6 2023-01-08 [1] RSPM (R 4.2.0)
## SingleCellExperiment * 1.20.0 2022-11-01 [1] Bioconductor
## spam 2.9-1 2022-08-07 [1] CRAN (R 4.2.2)
## sparseMatrixStats 1.10.0 2022-11-01 [1] Bioconductor
## SpatialExperiment * 1.8.0 2022-11-01 [1] Bioconductor
## spatialLIBD * 1.10.1 2022-12-01 [1] Bioconductor
## statmod 1.5.0 2023-01-06 [1] RSPM (R 4.2.0)
## stringi 1.7.12 2023-01-11 [2] RSPM (R 4.2.0)
## stringr 1.5.0 2022-12-02 [2] RSPM (R 4.2.0)
## styler 1.9.0 2023-01-15 [1] RSPM (R 4.2.0)
## SummarizedExperiment * 1.28.0 2022-11-01 [1] Bioconductor
## tibble 3.1.8 2022-07-22 [2] RSPM (R 4.2.0)
## tidyr 1.3.0 2023-01-24 [1] RSPM (R 4.2.0)
## tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.2)
## usethis * 2.1.6 2022-05-25 [2] RSPM (R 4.2.0)
## utf8 1.2.3 2023-01-31 [2] RSPM (R 4.2.0)
## vctrs 0.5.2 2023-01-23 [2] RSPM (R 4.2.0)
## vipor 0.4.5 2017-03-22 [1] CRAN (R 4.2.2)
## viridis 0.6.2 2021-10-13 [1] CRAN (R 4.2.2)
## viridisLite 0.4.1 2022-08-22 [1] CRAN (R 4.2.2)
## withr 2.5.0 2022-03-03 [2] RSPM (R 4.2.0)
## xfun 0.37 2023-01-31 [2] RSPM (R 4.2.0)
## XML 3.99-0.13 2022-12-04 [1] CRAN (R 4.2.2)
## xml2 1.3.3 2021-11-30 [2] RSPM (R 4.2.0)
## xtable 1.8-4 2019-04-21 [2] RSPM (R 4.2.0)
## XVector 0.38.0 2022-11-01 [1] Bioconductor
## yaml 2.3.7 2023-01-23 [2] RSPM (R 4.2.0)
## zlibbioc 1.44.0 2022-11-01 [1] Bioconductor
##
## [1] /__w/_temp/Library
## [2] /usr/local/lib/R/site-library
## [3] /usr/local/lib/R/library
##
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────proc.time()## user system elapsed
## 15.111 0.890 15.887This book was last updated at 2023-02-03 00:09:47.
License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.