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Uploading the images into the public domain is a very important part of the research process. I will upload image files to the [Image Data Resource](https://idr.openmicroscopy.org/) and add URL and me…
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In #83, I add code that performs this update.
## Summary
There appear to be substantial plate effects in the Repurposing Hub data, at least in UMAP space and using consensus DMSO data.
## DMS…
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To whom it may concern,
I run cellbender on a scRNA-Seq+CRISPR dataset derived from iPSCs.
I used the cellranger output in the folder filtered_feature_bc_matrix as an input for cellbender.
The ce…
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Hi,
Thanks so much for making this code available and usable!
In your NG manuscript, you look at some different options for using H3K27ac HiChIP, as well as including quantitative DHS signal. …
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## Issue
There are two issues. First, feature barcode syntax. Second, combining VDJ workflow with new scRNAExpression-CellRangerFastq workflow.
### Feature Barcode
Currently, FONDA uses 'old' cel…
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while looking into #1159, I noticed that these three nodes in KG2.3.4 have the name "LAP", but the first item in their `synonym` fields is TGFB_, which seemed slightly odd. then I noticed that if you …
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For any summer school suggestion that should be added to the list, please write a comment with the following information ;
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PhABC updated
4 years ago
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Hi,
I'm analyzing some single-cell RNA-seq data from a pooled CRISPR-screen. Using the known target genes of well understood CRISPR interference perturbations we compared different DE methods, and …
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I had
I‘d used CRISPRessoPooled for CRISPR analysis of 7000 amplicons. but get the following error:
merge reads, mapping and the intermediate bam file looks fine, but something wrong with samtoo…