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### If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.
#292
### Describe the goals of the changes to the analysis module.
Now that we have …
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Hi @danielsf,
I'm creating a new thread here, so we can continue our conversation regarding the marker genes that are used during the mapping process.
I followed your instructions in #10 in orde…
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In [Chapter 6 Marker detection, redux](https://bioconductor.org/books/3.13/OSCA.advanced/marker-detection-redux.html#marker-detection-redux) there is recommendation against limma-style analysis. I won…
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### Context
During eval, users looking at the SingleR and CellAssign cell type predictions were confused because their predictions differed so much. They were trying to figure out which one they …
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Hello, Mr. Tang
I want to perform collinearity analysis based on the mummer result coords file, in my opinion, this requires converting the coords file to a blast file, but I didn't convert it succes…
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Hi, thanks for your excellent tool!
I am wondering about the choice of plink. Should I use the same chr in step1 and step2&3 or just randomly choose in step1? Because I noticed that step1 used chr1 p…
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I was running DEnrichRPlot using my SCT assay after the PrepSCTFindMarkers. The data didn't quite make sense, so I reran it under the "RNA" assay. The data was drastically different (honestly made mor…
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Hi, I was just wondering if there is a way to add an extra gene(s)on top of 61 marker genes, in the core gene list before we run the analysis? Thanks, Sandeep
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Dear authors
I recently came across the publication "Epigenetic regulation during cancer transitions across 11 tumor types" and was impressed by the massive scale analysis you have performed.
I…
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Hi,
I am trying to analyze a dataset that includes 10 single cell experiments and about 66,000 cells. The actual set of cells I'm interested in is a small group of those, of about 7,000 cells. Wit…