Intro RNA-seq LCG-UNAM 2021
Overview
Here you can find the files for the February 2021 introduction to R, RStudio and RNA-sequencing (RNA-seq) course for LCG-UNAM at CCG-UNAM (February 23-26, 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_2021') or view online at lcolladotor.github.io/rnaseq_LCG-UNAM_2021.
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.org/about/code-of-conduct/.
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 23:
- Wednesday February 24:
- 9-11 am: expression data R/Bioconductor objects and visualization: SummarizedExperiment and iSEE
- 12-2 pm: Downloading RNA-seq data using recount3
- Thursday February 25:
- 9-11 am: statistical models with ExploreModelMatrix
- 12-2 pm: differential expression analysis with limma
- Friday February 26:
- 9-11 am: Review session
- 12-2 pm: spatial transcriptomics with spatialLIBD + open discussion (career paths, networking, etc)
External links
Course Prerequisites
Install R 4.0.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",
"postcards",
"pryr",
"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 1.4 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 student’s self evaluation (10%), the evaluation by each TA (15% each), your participation as evaluated by the instructor (10%), your public work (20%) and your final project (30%).
Projects, public work and notes are due at 9 am US Eastern on Monday March 1st, though we recommend doing any work related to this course by Friday February 26th.
R session information
Details on the R version used for making this book. The source code is available at lcolladotor/rnaseq_LCG-UNAM_2021.
## Load the package at the top of your script
library("sessioninfo")
## Utilities
library("BiocStyle")
library("biocthis")
library("here")
library("postcards")
library("pryr")
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")## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.0.3 (2020-10-10)
## os Ubuntu 20.04.1 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2021-03-04
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date lib source
## AnnotationDbi 1.52.0 2020-10-27 [1] Bioconductor
## AnnotationHub 2.22.0 2020-10-27 [1] Bioconductor
## assertthat 0.2.1 2019-03-21 [2] RSPM (R 4.0.0)
## attempt 0.3.1 2020-05-03 [1] RSPM (R 4.0.0)
## backports 1.2.1 2020-12-09 [1] RSPM (R 4.0.3)
## beachmat 2.6.4 2020-12-20 [1] Bioconductor
## beeswarm 0.2.3 2016-04-25 [1] RSPM (R 4.0.0)
## benchmarkme 1.0.6 2021-02-26 [1] RSPM (R 4.0.3)
## benchmarkmeData 1.0.4 2020-04-23 [1] RSPM (R 4.0.3)
## Biobase * 2.50.0 2020-10-27 [1] Bioconductor
## BiocFileCache 1.14.0 2020-10-27 [1] Bioconductor
## BiocGenerics * 0.36.0 2020-10-27 [1] Bioconductor
## BiocManager * 1.30.10 2019-11-16 [2] CRAN (R 4.0.3)
## BiocNeighbors 1.8.2 2020-12-07 [1] Bioconductor
## BiocParallel 1.24.1 2020-11-06 [1] Bioconductor
## BiocSingular 1.6.0 2020-10-27 [1] Bioconductor
## BiocStyle * 2.18.1 2020-11-24 [1] Bioconductor
## biocthis * 1.0.10 2021-02-26 [1] Bioconductor
## BiocVersion 3.12.0 2020-04-27 [2] Bioconductor
## Biostrings 2.58.0 2020-10-27 [1] Bioconductor
## bit 4.0.4 2020-08-04 [1] RSPM (R 4.0.3)
## bit64 4.0.5 2020-08-30 [1] RSPM (R 4.0.3)
## bitops 1.0-6 2013-08-17 [1] RSPM (R 4.0.3)
## blob 1.2.1 2020-01-20 [1] RSPM (R 4.0.3)
## bmp 0.3 2017-09-11 [1] RSPM (R 4.0.3)
## bookdown 0.21 2020-10-13 [1] RSPM (R 4.0.2)
## bslib 0.2.4 2021-01-25 [1] RSPM (R 4.0.3)
## cachem 1.0.4 2021-02-13 [2] RSPM (R 4.0.3)
## Cairo 1.5-12.2 2020-07-07 [1] RSPM (R 4.0.3)
## circlize 0.4.12 2021-01-08 [1] RSPM (R 4.0.3)
## cli 2.3.1 2021-02-23 [2] RSPM (R 4.0.3)
## clue 0.3-58 2020-12-03 [1] RSPM (R 4.0.3)
## cluster 2.1.1 2021-02-14 [3] RSPM (R 4.0.3)
## codetools 0.2-18 2020-11-04 [3] RSPM (R 4.0.3)
## colorspace 2.0-0 2020-11-11 [1] RSPM (R 4.0.3)
## colourpicker 1.1.0 2020-09-14 [1] RSPM (R 4.0.2)
## ComplexHeatmap 2.6.2 2020-11-12 [1] Bioconductor
## config 0.3.1 2020-12-17 [1] RSPM (R 4.0.3)
## cowplot 1.1.1 2020-12-30 [1] RSPM (R 4.0.3)
## crayon 1.4.1 2021-02-08 [2] RSPM (R 4.0.3)
## curl 4.3 2019-12-02 [2] RSPM (R 4.0.0)
## data.table 1.14.0 2021-02-21 [1] RSPM (R 4.0.3)
## DBI 1.1.1 2021-01-15 [1] RSPM (R 4.0.3)
## dbplyr 2.1.0 2021-02-03 [1] RSPM (R 4.0.3)
## DelayedArray 0.16.2 2021-02-26 [1] Bioconductor
## DelayedMatrixStats 1.12.3 2021-02-03 [1] Bioconductor
## desc 1.2.0 2018-05-01 [2] RSPM (R 4.0.0)
## digest 0.6.27 2020-10-24 [2] RSPM (R 4.0.3)
## dockerfiler 0.1.3 2019-03-19 [1] RSPM (R 4.0.0)
## doParallel 1.0.16 2020-10-16 [1] RSPM (R 4.0.3)
## dotCall64 1.0-1 2021-02-11 [1] RSPM (R 4.0.3)
## dplyr 1.0.4 2021-02-02 [1] RSPM (R 4.0.3)
## DT 0.17 2021-01-06 [2] RSPM (R 4.0.3)
## edgeR * 3.32.1 2021-01-14 [1] Bioconductor
## ellipsis 0.3.1 2020-05-15 [2] RSPM (R 4.0.0)
## evaluate 0.14 2019-05-28 [2] RSPM (R 4.0.0)
## ExperimentHub 1.16.0 2020-10-27 [1] Bioconductor
## ExploreModelMatrix * 1.2.0 2020-10-27 [1] Bioconductor
## fansi 0.4.2 2021-01-15 [2] RSPM (R 4.0.3)
## fastmap 1.1.0 2021-01-25 [2] RSPM (R 4.0.3)
## fields 11.6 2020-10-09 [1] RSPM (R 4.0.3)
## foreach 1.5.1 2020-10-15 [1] RSPM (R 4.0.3)
## fs 1.5.0 2020-07-31 [2] RSPM (R 4.0.2)
## generics 0.1.0 2020-10-31 [1] RSPM (R 4.0.3)
## GenomeInfoDb * 1.26.2 2020-12-08 [1] Bioconductor
## GenomeInfoDbData 1.2.4 2021-02-19 [1] Bioconductor
## GenomicAlignments 1.26.0 2020-10-27 [1] Bioconductor
## GenomicRanges * 1.42.0 2020-10-27 [1] Bioconductor
## GetoptLong 1.0.5 2020-12-15 [1] RSPM (R 4.0.3)
## ggbeeswarm 0.6.0 2017-08-07 [1] RSPM (R 4.0.0)
## ggplot2 * 3.3.3 2020-12-30 [1] RSPM (R 4.0.3)
## ggrepel 0.9.1 2021-01-15 [1] RSPM (R 4.0.3)
## GlobalOptions 0.1.2 2020-06-10 [1] RSPM (R 4.0.3)
## glue 1.4.2 2020-08-27 [2] RSPM (R 4.0.2)
## golem 0.2.1 2020-03-05 [1] RSPM (R 4.0.0)
## gridExtra 2.3 2017-09-09 [1] RSPM (R 4.0.3)
## gtable 0.3.0 2019-03-25 [1] RSPM (R 4.0.3)
## here * 1.0.1 2020-12-13 [1] RSPM (R 4.0.3)
## htmltools 0.5.1.1 2021-01-22 [2] RSPM (R 4.0.3)
## htmlwidgets 1.5.3 2020-12-10 [2] RSPM (R 4.0.3)
## httpuv 1.5.5 2021-01-13 [1] RSPM (R 4.0.3)
## httr 1.4.2 2020-07-20 [2] RSPM (R 4.0.2)
## igraph 1.2.6 2020-10-06 [1] RSPM (R 4.0.3)
## interactiveDisplayBase 1.28.0 2020-10-27 [1] Bioconductor
## IRanges * 2.24.1 2020-12-12 [1] Bioconductor
## irlba 2.3.3 2019-02-05 [1] RSPM (R 4.0.3)
## iSEE * 2.2.4 2021-02-01 [1] Bioconductor
## iterators 1.0.13 2020-10-15 [1] RSPM (R 4.0.3)
## jpeg 0.1-8.1 2019-10-24 [1] RSPM (R 4.0.3)
## jquerylib 0.1.3 2020-12-17 [1] RSPM (R 4.0.3)
## jsonlite 1.7.2 2020-12-09 [2] RSPM (R 4.0.3)
## knitr 1.31 2021-01-27 [2] RSPM (R 4.0.3)
## later 1.1.0.1 2020-06-05 [2] RSPM (R 4.0.2)
## lattice 0.20-41 2020-04-02 [3] CRAN (R 4.0.3)
## lazyeval 0.2.2 2019-03-15 [2] RSPM (R 4.0.0)
## lifecycle 1.0.0 2021-02-15 [2] RSPM (R 4.0.3)
## limma * 3.46.0 2020-10-27 [1] Bioconductor
## locfit 1.5-9.4 2020-03-25 [1] RSPM (R 4.0.3)
## magrittr 2.0.1 2020-11-17 [2] RSPM (R 4.0.3)
## maps 3.3.0 2018-04-03 [1] RSPM (R 4.0.3)
## MASS 7.3-53.1 2021-02-12 [3] RSPM (R 4.0.3)
## Matrix 1.3-2 2021-01-06 [3] RSPM (R 4.0.3)
## MatrixGenerics * 1.2.1 2021-01-30 [1] Bioconductor
## matrixStats * 0.58.0 2021-01-29 [1] RSPM (R 4.0.3)
## memoise 2.0.0 2021-01-26 [2] RSPM (R 4.0.3)
## mgcv 1.8-34 2021-02-16 [3] RSPM (R 4.0.3)
## mime 0.10 2021-02-13 [2] RSPM (R 4.0.3)
## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.0.3)
## munsell 0.5.0 2018-06-12 [1] RSPM (R 4.0.3)
## nlme 3.1-152 2021-02-04 [3] RSPM (R 4.0.3)
## patchwork * 1.1.1 2020-12-17 [1] RSPM (R 4.0.3)
## pheatmap * 1.0.12 2019-01-04 [1] RSPM (R 4.0.3)
## pillar 1.5.0 2021-02-22 [2] RSPM (R 4.0.3)
## pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.0.0)
## pkgload 1.2.0 2021-02-23 [2] RSPM (R 4.0.3)
## plotly 4.9.3 2021-01-10 [1] RSPM (R 4.0.3)
## png 0.1-7 2013-12-03 [1] RSPM (R 4.0.3)
## Polychrome 1.2.6 2020-11-11 [1] RSPM (R 4.0.3)
## postcards * 0.2.0 2021-01-06 [1] RSPM (R 4.0.3)
## promises 1.2.0.1 2021-02-11 [2] RSPM (R 4.0.3)
## pryr * 0.1.4 2018-02-18 [1] RSPM (R 4.0.3)
## purrr 0.3.4 2020-04-17 [2] RSPM (R 4.0.0)
## R.methodsS3 1.8.1 2020-08-26 [1] RSPM (R 4.0.3)
## R.oo 1.24.0 2020-08-26 [1] RSPM (R 4.0.3)
## R.utils 2.10.1 2020-08-26 [1] RSPM (R 4.0.3)
## R6 2.5.0 2020-10-28 [2] RSPM (R 4.0.3)
## rappdirs 0.3.3 2021-01-31 [2] RSPM (R 4.0.3)
## RColorBrewer * 1.1-2 2014-12-07 [1] RSPM (R 4.0.3)
## Rcpp 1.0.6 2021-01-15 [2] RSPM (R 4.0.3)
## RCurl 1.98-1.2 2020-04-18 [1] RSPM (R 4.0.3)
## readbitmap 0.1.5 2018-06-27 [1] RSPM (R 4.0.3)
## recount3 * 1.0.7 2021-02-11 [1] Bioconductor
## remotes 2.2.0 2020-07-21 [2] RSPM (R 4.0.2)
## rintrojs 0.2.2 2019-05-29 [1] RSPM (R 4.0.0)
## rjson 0.2.20 2018-06-08 [1] RSPM (R 4.0.3)
## rlang 0.4.10 2020-12-30 [2] RSPM (R 4.0.3)
## rmarkdown 2.7 2021-02-19 [1] RSPM (R 4.0.3)
## roxygen2 7.1.1 2020-06-27 [2] RSPM (R 4.0.2)
## rprojroot 2.0.2 2020-11-15 [2] RSPM (R 4.0.3)
## Rsamtools 2.6.0 2020-10-27 [1] Bioconductor
## RSQLite 2.2.3 2021-01-24 [1] RSPM (R 4.0.3)
## rstudioapi 0.13 2020-11-12 [2] RSPM (R 4.0.3)
## rsvd 1.0.3 2020-02-17 [1] RSPM (R 4.0.0)
## rtracklayer 1.50.0 2020-10-27 [1] Bioconductor
## S4Vectors * 0.28.1 2020-12-09 [1] Bioconductor
## sass 0.3.1 2021-01-24 [1] RSPM (R 4.0.3)
## scales 1.1.1 2020-05-11 [1] RSPM (R 4.0.3)
## scater 1.18.6 2021-02-26 [1] Bioconductor
## scatterplot3d 0.3-41 2018-03-14 [1] RSPM (R 4.0.3)
## scuttle 1.0.4 2020-12-17 [1] Bioconductor
## sessioninfo * 1.1.1 2018-11-05 [1] RSPM (R 4.0.3)
## shape 1.4.5 2020-09-13 [1] RSPM (R 4.0.3)
## shiny 1.6.0 2021-01-25 [1] RSPM (R 4.0.3)
## shinyAce 0.4.1 2019-09-24 [1] RSPM (R 4.0.0)
## shinydashboard 0.7.1 2018-10-17 [1] RSPM (R 4.0.3)
## shinyjs 2.0.0 2020-09-09 [1] RSPM (R 4.0.3)
## shinyWidgets 0.5.7 2021-02-03 [1] RSPM (R 4.0.3)
## SingleCellExperiment * 1.12.0 2020-10-27 [1] Bioconductor
## spam 2.6-0 2020-12-14 [1] RSPM (R 4.0.3)
## sparseMatrixStats 1.2.1 2021-02-02 [1] Bioconductor
## SpatialExperiment 1.0.0 2020-10-27 [1] Bioconductor
## spatialLIBD * 1.2.1 2020-12-21 [1] Bioconductor
## stringi 1.5.3 2020-09-09 [2] RSPM (R 4.0.2)
## stringr 1.4.0 2019-02-10 [2] RSPM (R 4.0.0)
## styler 1.3.2 2020-02-23 [1] RSPM (R 4.0.3)
## SummarizedExperiment * 1.20.0 2020-10-27 [1] Bioconductor
## testthat 3.0.2 2021-02-14 [2] RSPM (R 4.0.3)
## tibble 3.1.0 2021-02-25 [2] RSPM (R 4.0.3)
## tidyr 1.1.2 2020-08-27 [1] RSPM (R 4.0.3)
## tidyselect 1.1.0 2020-05-11 [1] RSPM (R 4.0.3)
## tiff 0.1-7 2021-03-02 [1] RSPM (R 4.0.3)
## usethis * 2.0.1 2021-02-10 [1] RSPM (R 4.0.3)
## utf8 1.1.4 2018-05-24 [2] RSPM (R 4.0.0)
## vctrs 0.3.6 2020-12-17 [2] RSPM (R 4.0.3)
## vipor 0.4.5 2017-03-22 [1] RSPM (R 4.0.0)
## viridis 0.5.1 2018-03-29 [1] RSPM (R 4.0.3)
## viridisLite 0.3.0 2018-02-01 [1] RSPM (R 4.0.3)
## withr 2.4.1 2021-01-26 [2] RSPM (R 4.0.3)
## xfun 0.21 2021-02-10 [2] RSPM (R 4.0.3)
## XML 3.99-0.5 2020-07-23 [1] RSPM (R 4.0.3)
## xml2 1.3.2 2020-04-23 [2] RSPM (R 4.0.0)
## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.0.3)
## XVector 0.30.0 2020-10-27 [1] Bioconductor
## yaml 2.2.1 2020-02-01 [2] RSPM (R 4.0.0)
## zlibbioc 1.36.0 2020-10-27 [1] Bioconductor
##
## [1] /__w/_temp/Library
## [2] /usr/local/lib/R/site-library
## [3] /usr/local/lib/R/library## user system elapsed
## 17.707 0.889 18.633This book was last updated at 2021-03-04 14:48:02.
License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.