RNAseqmixture

A python module to correct (ajust/deconvolute) for contamination of primary cell RNAseq with other cell types (eg. Macrophages).

No RNAseq of primary cells is pure - there are always other cell types sequenced within your sample. Given your purest sample(s) (=reference) and samples consisting just of the likely contaminations, this module attempts to correct for the contamination.

How much contamination is present is assessed based on a number of genes that are specific for your contamination - they should not show any expression in the pure reference.

For details see, Reinartz, Finkernagel et al., Genome Biol . 2016 May 23;17(1):108. doi: 10.1186/s13059-016-0956-6. A transcriptome-based global map of signaling pathways in the ovarian cancer microenvironment associated with clinical outcome