User: V

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V230
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230
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UK/London
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3 days, 12 hours ago
Joined:
4 years, 9 months ago
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Posts by V

<prev • 95 results • page 1 of 10 • next >
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Comment: C: pre-mRNA GTF reference for 10x
... Thank you I will try this out :) ...
written 3 days ago by V230
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Answer: C: KEGG pathway gene lists differ between sources
... I would personally trust KEGG over MsigDB as it tends to be better curated from my experience. A different solution would be looking directly at GO (http://geneontology.org/) You can look at curated gene sets and filter it on various parameters, including showing only genes that have experimental ...
written 3 days ago by V230
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Comment: C: pre-mRNA GTF reference for 10x
... Thanks for modifying initial post to show more detail @ATpoint. Would you happen to have a solution to this or could offer some clarification? :( ...
written 3 days ago by V230
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pre-mRNA GTF reference for 10x
... Hello, Would anyone in the community have a pre-mRNA reference GTF they would be willing to share? (mm10 and GRCh38) Or could point me towards the direction of finding one if they are aware if someone has made theirs available online? I'd like to be able to map my data to be able to detect intron ...
gtf singlecellrnaseq rna singlecell velocity written 4 days ago by V230 • updated 3 days ago by piyushjo470
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Comment: C: Can not detect spliced / unspliced counts
... I literally only did : adata = scv.read('matrix.mtx', cache=True) After obviously importing all the necessary packages. The error above pops up after doing that. The other consideration I had is that our genomics core uses the default (10xgenomics provided) GTF for GRCh38, and this does not s ...
written 4 days ago by V230
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Can not detect spliced / unspliced counts
... Hello, I keep running into an error whenever trying to run an scVelo analysis, once my data is loaded (tried different formats, like mtx and csv), I get the error WARNING: Could not find spliced / unspliced counts. I have generated these files directly from the barcodes.tsv, genes.tsv, and m ...
rnaseq rna velocity scvelo written 4 days ago by V230
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Comment: C: Running scVelo on Seurat
... I get this error when attempting "as.loom" Error in loomR::create(filename = filename, data = data[feature.order, : unused arguments (feature.attrs = as.list(x = meta.feature), transpose = TRUE, calc.count = FALSE, max.size = max.size, verbose = verbose) Have updated my Hdf5r and LoomR ...
written 5 days ago by V230
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Running scVelo on Seurat
... Hello, I’m trying to run scVelo on my dataset but I’m running into some issues and was wondering if you could help me. I have done my analysis on Seurat, and have subset and re-analysed sub-clusters and would like to run scVelo on those sub-clusters. Im trying to run it following this pipeline ...
singlecell velocity rna-seq seurat written 5 days ago by V230
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Comment: C: Seurat FeaturePlot across stims
... Thanks, did it using the below, leaving the code below as reference if anyone else runs into something similar. Would still be good to know if there is a way of doing it using a plotting function rather than having to subset things. e14only <- subset(seurat.combined, subset = stim == c('X ...
written 13 days ago by V230
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Comment: C: scVelo on Seurat umap
... Thank you. Is the best way to output from Seurat the ‘asLoom’ command? I’ve tried various ways and getting different errors that’s why I resulted to re-analysing from scratch and then wanted to embed it. ...
written 13 days ago by V230

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