Question: Single cell RNA sequencing Seurat and Monocle
1
gravatar for bioinformatics.cancer
12 months ago by
United States
bioinformatics.cancer180 wrote:

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

ADD COMMENTlink modified 10 months ago by dppb0570 • written 12 months ago by bioinformatics.cancer180
3
gravatar for dppb05
10 months ago by
dppb0570
dppb0570 wrote:

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

ADD COMMENTlink written 10 months ago by dppb0570
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