function,parameter,value
CIBERSORT (historical scripts),signature_matrix,LM22.txt
CIBERSORT (historical scripts),perm,1000
CIBERSORT (historical scripts),QN,TRUE
FindMarkers (historical scripts),ident.1,Metastasis
FindMarkers (historical scripts),ident.2,Primary
FindMarkers (historical scripts),group.by,sample_class
Single-cell DEG display filter,p_val,<0.05
Single-cell DEG display filter,abs(avg_log2FC),>0.5
Single-cell DEG display filter,p_val_adj,<0.2
Single-cell whole-cell DEG display,upregulated sorting,avg_log2FC descending
Single-cell whole-cell DEG display,downregulated sorting,avg_log2FC ascending
Single-cell whole-cell DEG display,maximum genes per direction,100
Single-cell cell-type DEG display,sorting,p_val ascending
Single-cell cell-type DEG display,maximum genes per cell type,100
Marker summaries,library_size,all retained genes in the counts layer
Marker summaries,scale.factor,10000
Marker summaries,transformation,log1p
Marker summaries,detection,counts > 0
GSE205209 avereps,ID,retained gene identifiers
GSE205209 duplicateCorrelation,block,patient_id in patients with repeated specimens
GSE205209 lmFit,design,~0 + group (Primary and Metastasis)
GSE205209 lmFit,block,patient_id
GSE205209 lmFit,correlation,estimated consensus.correlation
GSE205209 makeContrasts,contrast,Metastasis-Primary
GSE205209 eBayes,trend,TRUE
GSE205209 topTable,number,Inf
GSE205209 topTable,sort.by,P
GSE205209 topTable,adjust.method,BH
GSE205209 PCA,center,TRUE
GSE205209 PCA,scale.,FALSE
Historical pipeline,arguments omitted from script calls,Package defaults in the software versions employed