| 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 | |