In wguo-research/scCancer: A package for automated processing of single cell RNA-seq data in cancer

r h.i.r h.ii Expression programs identification

In order to unsupervised identify potential expression program signatures, we apply non-negative matrix factorization (NMF) to the centralized and non-negative changed expression matrix. The input for number of identified programs (the rank in NMF) is r results$nmf.rank.

Following is the heatmap for identified cells' expression programs.

results$exprProgram.plot

(Hi-res image: view)

After this step, scCancer saved following results files to the folder 'expr.programs': * The left matrix W (genes * programs): W-gene-program.txt. * The right matrix H (programs * cells): H-program-cell.txt. * The relative genes of each programs: program.gene.value.txt.

h.ii <- h.ii + 1

wguo-research/scCancer documentation built on May 26, 2024, 9:12 p.m.