BOOKED OUT: 10X single-cell RNA-seq analysis workshop
Who: The course is aimed at advanced PhD students, postdoctoral researchers and principal investigators. Some basic R knowledge is assumed – this is not an introduction to R course. If you are not familiar with the R statistical programming language it is compulsory that you work through an introductory R course before you attend this workshop.
This workshop will cover single-cell RNA-seq analysis and assumes you have some familiarity with the more common analysis of bulk RNA-seq data. If you have no experience in analysing bulk RNA-seq data, we strongly recommend you also attend our RNA-seq Differential Gene Expression analysis in R workshop.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. Bringing your laptop charger is advised. R and a few specific software packages should be installed in advance. The 10X data to be analysed, the gene annotation file and the gene signature RData file should also be downloaded prior to the workshop to allow us time to troubleshoot any problems you may have.
1. Download R from https://cran.r-project.org/. The lastest version is recommended (version 3.6.0 for Windows and Mac OS X 10.11 and higher).
2. Install R packages by opening R and copying the following commands into your R console
if (!requireNamespace(“BiocManager”, quietly = TRUE))
BiocManager::install(c(“scran”, “monocle”, “vcd”))
3. Download the 10X single-cell RNA-seq data from GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2510617). The three data files required for the workshop are: GSM2510617_P7-barcodes.tsv.gz, GSM2510617_P7-genes.tsv.gz and GSM2510617_P7-matrix.mtx.gz, of which the download links are available at the bottom of the web page. Unzip the three data files and store them in the working directory (or a sub-folder under the working directory).
4. Download the mouse gene annotation file from http://bioinf.wehi.edu.au/edgeR/Mus_musculus.gene_info.gz and save it under the working directory. Note there is no need to unzip the file.
5. Download gene signatures from http://bioinf.wehi.edu.au/edgeR/BulkSignatures.RData and save it under the working directory.
6. Check downloads are correct by looking for any error messages when running the commands:
Important: If you have any trouble installing the software or packages, please contact us prior to the workshop.