Changes between Version 24 and Version 25 of SOP/scRNA-seq


Ignore:
Timestamp:
10/05/20 13:49:26 (4 years ago)
Author:
ibarrasa
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOP/scRNA-seq

    v24 v25  
    153153  * consider each cell as a sample
    154154  * aggregate counts across all cells in a group/cluster, and treat them as one sample
    155 Seurat has 2 functions "FindAllMarkers" and "FindMarkers" that work well as long as the fold change and percentage of cells expressing the gene thresholds are not relaxed from the defaults "logfc.threshold = 0.25, min.pct = 0.1." More stringent thresholds (MIN_LOGFOLD_CHANGE = 0.7,  MIN_PCT_CELLS_EXPR_GENE = .25) also work well.
     155Seurat has 2 functions "FindAllMarkers" and "FindMarkers" that work well as long as the fold change and percentage of cells expressing the gene thresholds are not too relaxed. We recommend logfc.threshold = 0.7, min.pct = .25.).
    156156  * example command to compare each cluster to all other clusters:
    157157{{{
     158MIN_LOGFOLD_CHANGE = 0.7
     159MIN_PCT_CELLS_EXPR_GENE = .25
    158160all.markers.pos.wilcox = FindAllMarkers(all_Filt,
    159161                                        min.pct = MIN_PCT_CELLS_EXPR_GENE,