search

LieberInstitute / spatialDLPFC

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
http://research.libd.org/spatialDLPFC/
19 stars 3 forks source link

make pseudobulked objects for DE analysis #61

Closed abspangler13 closed 2 years ago

abspangler13 commented 2 years ago

first part of this: https://jhu-genomics.slack.com/archives/C01EA7VDJNT/p1648751711386829 zoom: https://jhu-genomics.slack.com/archives/C029NB48G9K/p1648831514251679

  1. use aggregated across cells to pseudobulk on different k's
  2. normalize raw counts (edgeR::calcNormFactors() which I forget if scater::logNormCounts() uses internally)
  3. drop lowly expressed genes (jaffelab::expression_cutoff() or edgeR::filterByExpr())
  4. save these objects for later use

set up to run as an sge job for all values of k