search

parmejohn / scRNA-pipeline-UofM

scRNA-seq Pipeline for Drogemoller and Wright Labs
GNU General Public License v3.0
0 stars 2 forks source link

find a way to add co-variants to deseq2 analysis #45

Open parmejohn opened 1 month ago

parmejohn commented 3 weeks ago

https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html in the multi-factor designs section should be it

parmejohn commented 2 weeks ago

installed BiocManager::install("apeglm") to match seurat deseq2 method as seen from https://github.com/satijalab/seurat/issues/7764

parmejohn commented 2 weeks ago

added checking for highest ranking combination of the main conditions and the other factors when performing comparative analyses. should avoid linear combinations.

parmejohn commented 2 weeks ago

look for other papers and see how they deal with time-disease comparisons