single cell sequencing datasets batch effect

Question

[aarvaBioinfo]

hi all, I have 3 single cell sequencing datasets from different year and in the form of cell ranger output files as barcode.tsv, gene.tsv and matrix.mtx files for each sample then how can i remove batch effect from them for gene expression analysis. is anyone have experience for this ?

[897776177]

i have the same issue, would you please give me some suggestions? which software do you use? can you integrate different single cell datasets together?

thanks in advance xia

Answer 1

[Mark]

There are several tutorials and packages found online http://bioconductor.org/packages/devel/bioc/vignettes/batchelor/inst/doc/correction.html

There is BEER https://github.com/jumphone/BEER https://www.nature.com/articles/s41421-019-0114-x

There are more software found here: https://github.com/mdozmorov/scRNA-seq_notes#batch-effect-merging