Single cell RNA sequencing Seurat and Monocle

Question

[bioinformatics.cancer]

Hi, I am analyzing some single cell rna-seq data sets with Seurat and would like the follow up the analysis with cell trajectory analysis using monocle. In order to keep the analysis in sync I would like to use the pre-processed expression matrix in monocle (i.e., the normalized, scaled, transformed. and centered values). The raw expression data is in UMI counts. If I start from the raw input in monocle I end up getting a slightly different clustering. I read on the Seurat FAQ page that a seuratTomonocle function is forthcoming. I was wondering if someone has already done this with custom code or has experience with doing cell trajectory analysis in monocle following Seurat analysis and can help out with the steps. Thanks - Pankaj

Answer 1

[dppb05]

You can use monocle::importCDS function by passing your Seurat object as parameter.