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Hello,
I was wondering, is there a way to provide a structure along with the SHAPE reactivities, and predefine a color scheme (so that, for example, reactive bases above a certain value get a certa…
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Hi,
I've been gratefully using ExomePeak2 for my m6A differential methylation analyses.
Although I was focusing on eukaryotic hosts, I am interested in analyzing m6A in ssRNA & dsDNA viruses, and …
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We need to run an alignment on our FASTQ files or a subset of them to determine the strandedness; need to add this check to our quite of seq-tools checks
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Hi, I wonder if there is any function in celldancer which can generate the raw RNA velocity matrix. I intend to compare this method with other RNA velocity estimation method. Thanks a lot.
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Hi RMolania! Thanks for the very useful approach. I want to use RUV-III with PRPS for non-TCGA RNA-seq data, but I don't know how to process the non-TCGA RNA-seq data to use RUV-III with PRPS. Would y…
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Hi,
Thanks for the great package.
I'm trying to follow step 1 and when I get to
```
scglue.data.get_gene_annotation(
rna, gtf="gencode.vM25.chr_patch_hapl_scaff.annotation.gtf.gz",
…
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This additional function is necessary if SCTransform was used, otherwise we won't find any markers. We need to read a bit more on this. For now, I added the following code, just above `RunPrestoAll`:
…
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# 生信爱好者周刊(第 141 期):
这里记录每周值得分享的生信相关内容,周日发布。
本杂志开源(GitHub: [openbiox/weekly](https://github.com/openbiox/weekly)),欢迎提交 issue,投稿或推荐生信相关内容。
[「生信周刊讨论区」](https://github.com/openbiox/weekly/discuss…
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cancer cells classic-like should be cancer classical cells according to the PDAC consensus classification (basal-like and classical).
"bulk references" could be confusing. Suggestion instead: cell-ty…
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Hi BRAKER developers,
I've been using BRAKER3 with RNA-seq data produced from VARUS, on our university HPC using singularity.
The first step of GeneMark-ET runs fine then I get an error when tra…