Question: single cell sequencing datasets batch effect
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gravatar for aarvaBioinfo
2.0 years ago by
aarvaBioinfo10
aarvaBioinfo10 wrote:

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 ?

R • 1.0k views
ADD COMMENTlink modified 13 months ago by Mark800 • written 2.0 years ago by aarvaBioinfo10

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

ADD REPLYlink written 13 months ago by 8977761770
2
gravatar for Mark
13 months ago by
Mark800
Mark800 wrote:

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

ADD COMMENTlink written 13 months ago by Mark800
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