Tag: pseudotime

Single-cell delineation of lineage and genetic identity in the mouse brain

STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…

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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 ?…

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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…

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Trouble running Cyclum for my scRNA-seq analysis

I have been analyzing some mouse T cell scRNA-seq data for a few months now using mostly the Seurat pipeline run with default parameters, and I have noticed that regressing out the ‘S.Score’ and ‘G2M.Score’ obtained from default Seurat::CellCycleScoring seems to be insufficient to remove (seemingly large) variation originating from…

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Bioconductor – traviz (development version)

DOI: 10.18129/B9.bioc.traviz     This is the development version of traviz; to use it, please install the devel version of Bioconductor. Trajectory functions for visualization and interpretation. Bioconductor version: Development (3.14) traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in…

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heatmap of genes pseudotime in monoclle3

heatmap of genes pseudotime in monoclle3 0 Login before adding your answer. Traffic: 1946 users visited in the last hour Source link

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