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Tag: monocle2
smartseq2 RPKM data
Hi! I have smartseq2 RPKM data (already analysed with Seurat pipeline) and I want to do trajectory analysis of my cells. Having RPKM data I wondered whether I can use Monocle 3 or can it just be used with UMI data (10x) ? In Monocle2 it seemed to be possible…
TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development
Curation of early-embryo development single-cell RNA-seq data sets for studying cell-cell communication To identify and study eLRs, we collected public early embryo development scRNA-seq datasets from the mouse MII-oocyte stage to the late blastocyst stage to ensure that scRNA-seq datasets represented every stage of early embryo development. In addition, to…
Error in h(simpleError(msg, call)) in monocle2
Error in h(simpleError(msg, call)) in monocle2 0 Want to run monocle2 for a single cell RNAseq data processed using Seurat, but encountering following problem. library(monocle) Seurat An object of class Seurat 41445 features across 55683 samples within 1 assay Active assay: RNA (41445 features, 1850 variable features) 4 dimensional reductions…
Which trajectory method is better !?
Which trajectory method is better !? 2 Hello I was engaged with a basic problem. I have dataset consist ~2000 cells and composed 8-9 clusters using Seurat package, then I transfer Seurat object to the Monocle. I tried monocle2 and monocle3. The problem is, how to make the trajectory ?…
Extract root(start) and leaf(end) states programmatically in monocle2
Extract root(start) and leaf(end) states programmatically in monocle2 0 Dear bioinformaticians, do you know how to extract starting state and end states from the CDS in monocle2 ? I know I can detect them visually inspecting the States plot after I compute the pseudotime. I am asking if there is…