The material for this work was kindly borrowed with permission and adapted from the fantastic online course Analysis of single cell RNA-seq data from Vladimir Kiselev (wikiselev), Tallulah Andrews (talandrews), Jennifer Westoby (Jenni_Westoby), Davis McCarthy (davisjmcc), Maren Büttner (marenbuettner) and Martin Hemberg (m_hemberg).
The material in the course above covers about 1.5 days and we will be taking a subset of the material for our 2-3 hour workshop for 2018 BioInfoSummer where we will be discussing the statistical analysis and comprehension of single cell RNA-sequencing data in R/Bioconductor.
You will need to install the following R packages:
install.packages("devtools")
install.packages("BiocManager")
install.packages("RColorBrewer", "reshape2",
"matrixStats", "mclust", "pheatmap", "mvoutlier")
devtools::install_github("hemberg-lab/scRNA.seq.funcs")
devtools::install_github("theislab/kBET")
BiocManager::install(c("scater", "scran", "Rtsne", "sva",
"DESeq2", "edgeR", "SC3", "zinbwave"))
The orginal and complete course material is available at:
https://github.com/hemberg-lab/scRNA.seq.course
The adapted material for this course at BioInfoSummer 2018 is available at:
https://github.com/stephaniehicks/2018-bioinfosummer-scrnaseq
The course material is available on the course GitHub repository which can be cloned using
git clone https://github.com/stephaniehicks/2018-bioinfosummer-scrnaseq
The license from the original course material is licensed under GPL-3 and that license is maintained here. Anyone is welcome to go through the material in order to learn about analysis of scRNA-seq data. If you plan to use the material for your own teaching, the original authors have requested that they would appreciate it if you tell them about it in addition to providing a suitable citation. Please contact the original lead author Vladimir Kiselev.
The course is intended for those who have basic familiarity with Unix and the R scripting language. We will also assume that you are familiar with mapping and analyzing bulk RNA-seq data as well as with the commonly available computational tools.
If you have any comments, questions or suggestions about the original and complete course material, please contact Vladimir Kiselev.
If you have questions about the material presented in this course at BioInfoSummer 2018, you can reach me at Stephanie Hicks