Tag: scVelo

scVelo cell transitions from marker gene expressing cells

scVelo cell transitions from marker gene expressing cells 0 Hi Im working with scVelo and looking to match a subset of cells in one cluster with preferential cell state transitions and what gene(s) may underlie this connection. Currently we can do the following to put in specific cells from adata…

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Input data matrix from Seurat toolkit analysis for RNA velocity analysis using scvelo

Input data matrix from Seurat toolkit analysis for RNA velocity analysis using scvelo 0 Hi, I have done the scRNAseq analysis follwoing seurat toolkit vignette (SCTtransform + integrate + clustering) and now planning to run RNA velocity analysis using scvelo tool. Is it reasonable to use the SCT assay, data…

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Help with scvelo

Help with scvelo 0 Hi Biostars, I try to use scvelo but got this error message: scv.tl.velocity_graph(adata) ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (1, 4) + inhomogeneous part. This is a math error but…

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Scvelo vs Monocle3

Scvelo vs Monocle3 0 Hi Biostars, I tried to do trajectory analysis but got an error message here Help with error velocyto so I tried Monocle3 and I feel it was a lot faster and simpler than using scVelo/velocyto. However, with Monocle3, how can we know where the root note…

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The RNA velocity are opposite in ‘dynamical’ and ‘stochastic’ modes.

Hi When I run velocity using both ‘dynamical’ and ‘stochastic’ modes: import scvelo as scv import scanpy as sc scv.pp.moments(adata) scv.tl.velocity(adata, mode=”stochastic”) scv.tl.velocity_graph(adata) scv.pl.velocity_embedding_stream(adata, basis=”umap”, arrow_size = 1, density = 2, size = 50, arrow_style=”->”, color=”leiden_r1″, alpha = 0.2, dpi = 300, legend_loc=”on data”, integration_direction = ‘both’, arrow_color=”k”, figsize =…

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Converting hdf5 file to loom file

Converting hdf5 file to loom file 1 Hello, I am currently processing the single cell data. I have hdf5 file, however, I want the loom file for downstream analysis. Can anyone please suggest if there is a way to convert hdf5 to loom file format? Any help is highly appreciated….

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Cas9-mediated knockout of Ndrg2 enhances the regenerative potential of dendritic cells for wound healing

Ndrg2 expression is reduced in tolerogenic DCs To identify potential targets for gene editing in DCs, we compared transcriptomic profiles of treatment induced tolerogenic DCs, which confer a variety of clinical benefits11,12,13,14,15,16,17 with untreated DCs. Bone marrow-derived DCs were cultivated from wild-type (WT) mice (C57/BL6) according to standard protocols25. Vitamin…

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Getting unspliced counts for scRNA-seq data generated from cellranger aggr pipeline

Getting unspliced counts for scRNA-seq data generated from cellranger aggr pipeline 1 Hi everyone, I have 15 scRNA-seq samples that I have aggregated with cellranger aggr pipeline. My problem is that, I would like to use scVelo on my dataset. However, I will need the unspliced counts for this. I…

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Getting unspliced counts for my data generated from cellranger aggr pipeline

Getting unspliced counts for my data generated from cellranger aggr pipeline 0 Hi everyone, I have 15 scRNA-seq samples that I have aggregated with cellranger aggr pipeline. My problem is that, I would like to use scVelo on my dataset. However, I will need the unspliced counts for this. I…

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Identification of a regulatory pathway inhibiting adipogenesis via RSPO2

Integration of APC scRNA-seq data reveals heterogeneity of adipocyte progenitor cells In a previous study9, we defined Lin−Sca1+CD142+ APCs as adipogenesis regulatory (Areg) cells and demonstrated that these cells are both refractory toward adipogenesis and control adipocyte formation of APCs through paracrine signaling. In contrast, Merrick et. al.4 observed that Lin−CD142+ cells…

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