User¶

Import omicverse as:

import omicverse as ov

Bulk¶

module	reference
bulk.pyDEG	Different expression analysis
bulk.pyGSEA	Geneset enrichment analysis
bulk.pyTCGA	TCGA database preprocess
bulk.pyPPI	Protein-Protein interaction (PPI) analysis by String-db
bulk.pyWGCNA	WGCNA (Weighted gene co-expression network analysis)

module	reference
single.pySCSA	Celltype auto annotation with SCSA
single.MetaTiME	Celltype auto annotation with MetaTiME
single.pyVIA	Trajectory calculated with VIA
single.COSG	Marker genes filtered with COSG
single.scDrug	Drug response predict with scDrug
single.scGSEA	Pathway analysis with AUCell
single.cpdb	Cell interaction with CellPhoneDB
single.MOFA	Multi omics analysis by MOFA
single.pySIMBA	Batch correction with SIMBA
single.pyTOSICA	Celltype predicted from reference scRNA-seq

module	reference
bulk2single.BulkTrajBlend	bulk RNA-seq generate interrupt cell in scRNA-seq
bulk2single.Bulk2Single	Bulk RNA-seq to Single RNA-seq
bulk2single.Single2Spatial	Single RNA-seq to Spatial RNA-seq

module	reference
pp	preprocessing the scRNA-seq
qc	quantity control the scRNA-seq
plot	plot function