scRNA-seq data analysis - R

Question

[ja4123]

Hi! Could anyone suggest some tutorial how to do scRNA-seq data analysis in R given files:

• .tsv with barcodes
• .tsv with features
• and .mtx matrix

I am new in this and I will appreciate any help.

Answer 1

[Mensur Dlakic]

A simple Google search will give you many resources to explore.

• http://bioinf.wehi.edu.au/edgeR/10XWorkshop/10X.pdf
• http://bioinf.wehi.edu.au/edgeR/10XWorkshop/
• https://www.singlecellcourse.org/
• https://github.com/bishwaG/Single-cell-RNA-seq-data-analysis-2018
• https://satijalab.org/seurat/articles/get_started.html
• https://www.nature.com/articles/s41596-020-00409-w
• https://link.springer.com/protocol/10.1007%2F978-1-0716-1307-8_19

Answer 2

[ATpoint]

The best resource: https://bioconductor.org/books/release/OSCA/

Please google for loading mtx into R (hint, it is the readMM function from the Matrix package).