Intro RNA-seq LCG-UNAM 2022
Overview
Here you can find the files for the February 2022 introduction to R, RStudio and RNA-sequencing (RNA-seq) course for LCG-UNAM at CCG-UNAM (February 1-4, 2021). The rest of the chapters will be in Spanish.
Instructor:
Teach assistants:
Course Coordinators:
- Heladia Salgado
- Julio Collado Vides
Download the materials for this course with usethis::use_course('lcolladotor/rnaseq_LCG-UNAM_2022') or view online at lcolladotor.github.io/rnaseq_LCG-UNAM_2022.
Code of Conduct
We’ll follow the CDSB code of conduct comunidadbioinfo.github.io/codigo-de-conducta/ as well as version 1.0.1 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 February 1:
- Wednesday February 2:
- 9-11 am: expression data R/Bioconductor objects and visualization: SummarizedExperiment and iSEE
- 12-2 pm: Downloading RNA-seq data using recount3
- Thursday February 3:
- 9-11 am: statistical models with ExploreModelMatrix
- 12-2 pm: differential expression analysis with limma
- Friday February 4:
- 9-12 am: Review session + spatial transcriptomics with spatialLIBD
- 1-2 pm: open discussion (career paths, networking, etc)
External links
- Cursos LCG
- GitHub source code
- Zoom (ask)
- LCG-UNAM RStudio server
- CDSB.
- Slack CDSB Mexico, in particular the
intro_rnaseq_lcg_2022channel. You can join this Slack workspace through this link.
Course Prerequisites
Install R 4.1.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",
"spatialLIBD" ## Advanced
)
)You will also need to install RStudio version 2021.09 or newer.
Course Evaluation
- Participation
- (main evidence) written and/or verbal participation during sessions and break-out rooms
- (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 URL (gist, GitHub, …)
- (optional) a rendered Rmd file (RPubs, GitHub)
- (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.
The final grade will be a weighted average from the evaluation by each TA (15% each), your public work (30%) and your final project (40%).
Projects, public work and notes are due at 9 am US Eastern on Monday February 14th, though we recommend doing any work related to this course by Friday February 11th.
R session information
Details on the R version used for making this book. The source code is available at lcolladotor/rnaseq_LCG-UNAM_2022.
## 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("ggplot2")
library("patchwork")
library("pheatmap")
library("RColorBrewer")
## Advanced
library("spatialLIBD")## Reproducibility information
options(width = 120)
session_info()## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.2 (2021-11-01)
## os Ubuntu 20.04.3 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz UTC
## date 2022-02-04
## pandoc 2.14.0.3 @ /usr/local/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## AnnotationDbi 1.56.2 2021-11-09 [1] Bioconductor
## AnnotationHub 3.2.1 2022-01-23 [1] Bioconductor
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## beachmat 2.10.0 2021-10-26 [1] Bioconductor
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## benchmarkme 1.0.7 2021-03-21 [1] RSPM (R 4.1.0)
## benchmarkmeData 1.0.4 2020-04-23 [1] RSPM (R 4.1.0)
## Biobase * 2.54.0 2021-10-26 [1] Bioconductor
## BiocFileCache 2.2.1 2022-01-23 [1] Bioconductor
## BiocGenerics * 0.40.0 2021-10-26 [1] Bioconductor
## BiocIO 1.4.0 2021-10-26 [1] Bioconductor
## BiocManager 1.30.16 2021-06-15 [2] CRAN (R 4.1.2)
## BiocNeighbors 1.12.0 2021-10-26 [1] Bioconductor
## BiocParallel 1.28.3 2021-12-09 [1] Bioconductor
## BiocSingular 1.10.0 2021-10-26 [1] Bioconductor
## BiocStyle * 2.22.0 2021-10-26 [1] Bioconductor
## biocthis * 1.4.0 2021-10-26 [1] Bioconductor
## BiocVersion 3.14.0 2021-05-19 [2] Bioconductor
## Biostrings 2.62.0 2021-10-26 [1] Bioconductor
## bit 4.0.4 2020-08-04 [1] RSPM (R 4.1.0)
## bit64 4.0.5 2020-08-30 [1] RSPM (R 4.1.0)
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## DBI 1.1.2 2021-12-20 [1] RSPM (R 4.1.0)
## dbplyr 2.1.1 2021-04-06 [1] RSPM (R 4.1.0)
## DelayedArray 0.20.0 2021-10-26 [1] Bioconductor
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## dplyr 1.0.7 2021-06-18 [2] RSPM (R 4.1.0)
## dqrng 0.3.0 2021-05-01 [1] RSPM (R 4.1.0)
## DropletUtils 1.14.2 2022-01-09 [1] Bioconductor
## DT 0.20 2021-11-15 [1] RSPM (R 4.1.0)
## edgeR * 3.36.0 2021-10-26 [1] Bioconductor
## ellipsis 0.3.2 2021-04-29 [2] RSPM (R 4.1.0)
## evaluate 0.14 2019-05-28 [2] RSPM (R 4.1.0)
## ExperimentHub 2.2.1 2022-01-23 [1] Bioconductor
## ExploreModelMatrix * 1.6.0 2021-10-26 [1] Bioconductor
## fansi 1.0.2 2022-01-14 [2] RSPM (R 4.1.0)
## fastmap 1.1.0 2021-01-25 [2] RSPM (R 4.1.0)
## fields 13.3 2021-10-30 [1] RSPM (R 4.1.0)
## filelock 1.0.2 2018-10-05 [1] RSPM (R 4.1.0)
## foreach 1.5.2 2022-02-02 [1] RSPM (R 4.1.0)
## fs 1.5.2 2021-12-08 [2] RSPM (R 4.1.0)
## generics 0.1.2 2022-01-31 [2] RSPM (R 4.1.0)
## GenomeInfoDb * 1.30.1 2022-01-30 [1] Bioconductor
## GenomeInfoDbData 1.2.7 2022-01-31 [1] Bioconductor
## GenomicAlignments 1.30.0 2021-10-26 [1] Bioconductor
## GenomicRanges * 1.46.1 2021-11-18 [1] Bioconductor
## GetoptLong 1.0.5 2020-12-15 [1] RSPM (R 4.1.0)
## ggbeeswarm 0.6.0 2017-08-07 [1] RSPM (R 4.1.0)
## ggplot2 * 3.3.5 2021-06-25 [1] RSPM (R 4.1.0)
## ggrepel 0.9.1 2021-01-15 [1] RSPM (R 4.1.0)
## GlobalOptions 0.1.2 2020-06-10 [1] RSPM (R 4.1.0)
## glue 1.6.1 2022-01-22 [2] RSPM (R 4.1.0)
## golem 0.3.1 2021-04-17 [1] RSPM (R 4.1.0)
## gridExtra 2.3 2017-09-09 [1] RSPM (R 4.1.0)
## gtable 0.3.0 2019-03-25 [1] RSPM (R 4.1.0)
## HDF5Array 1.22.1 2021-11-14 [1] Bioconductor
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## IRanges * 2.28.0 2021-10-26 [1] Bioconductor
## irlba 2.3.5 2021-12-06 [1] RSPM (R 4.1.0)
## iSEE * 2.6.0 2021-10-26 [1] Bioconductor
## iterators 1.0.13 2020-10-15 [1] RSPM (R 4.1.0)
## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.1.0)
## jsonlite 1.7.3 2022-01-17 [2] RSPM (R 4.1.0)
## KEGGREST 1.34.0 2021-10-26 [1] Bioconductor
## knitr 1.37 2021-12-16 [2] RSPM (R 4.1.0)
## later 1.3.0 2021-08-18 [1] RSPM (R 4.1.0)
## lattice 0.20-45 2021-09-22 [3] CRAN (R 4.1.2)
## lazyeval 0.2.2 2019-03-15 [1] RSPM (R 4.1.0)
## lifecycle 1.0.1 2021-09-24 [2] RSPM (R 4.1.0)
## limma * 3.50.0 2021-10-26 [1] Bioconductor
## lobstr * 1.1.1 2019-07-02 [1] RSPM (R 4.1.0)
## locfit 1.5-9.4 2020-03-25 [1] RSPM (R 4.1.0)
## magick 2.7.3 2021-08-18 [1] RSPM (R 4.1.0)
## magrittr 2.0.2 2022-01-26 [2] RSPM (R 4.1.0)
## maps 3.4.0 2021-09-25 [1] RSPM (R 4.1.0)
## MASS 7.3-55 2022-01-13 [3] RSPM (R 4.1.0)
## Matrix 1.4-0 2021-12-08 [3] RSPM (R 4.1.0)
## MatrixGenerics * 1.6.0 2021-10-26 [1] Bioconductor
## matrixStats * 0.61.0 2021-09-17 [1] RSPM (R 4.1.0)
## memoise 2.0.1 2021-11-26 [2] RSPM (R 4.1.0)
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## nlme 3.1-155 2022-01-13 [3] RSPM (R 4.1.0)
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## pillar 1.7.0 2022-02-01 [2] RSPM (R 4.1.0)
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## promises 1.2.0.1 2021-02-11 [1] RSPM (R 4.1.0)
## ps 1.6.0 2021-02-28 [2] RSPM (R 4.1.0)
## purrr 0.3.4 2020-04-17 [2] RSPM (R 4.1.0)
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## R.methodsS3 1.8.1 2020-08-26 [1] RSPM (R 4.1.0)
## R.oo 1.24.0 2020-08-26 [1] RSPM (R 4.1.0)
## R.utils 2.11.0 2021-09-26 [1] RSPM (R 4.1.0)
## R6 2.5.1 2021-08-19 [2] RSPM (R 4.1.0)
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## rmarkdown 2.11 2021-09-14 [1] RSPM (R 4.1.0)
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## ScaledMatrix 1.2.0 2021-10-26 [1] Bioconductor
## scales 1.1.1 2020-05-11 [1] RSPM (R 4.1.0)
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## sparseMatrixStats 1.6.0 2021-10-26 [1] Bioconductor
## SpatialExperiment * 1.4.0 2021-10-26 [1] Bioconductor
## spatialLIBD * 1.6.5 2022-01-12 [1] Bioconductor
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##
## [1] /__w/_temp/Library
## [2] /usr/local/lib/R/site-library
## [3] /usr/local/lib/R/library
##
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────proc.time()## user system elapsed
## 16.025 0.899 16.850This book was last updated at 2022-02-04 17:18:27.
License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.