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Hello,
I have a question about measuring the concordance between bulk and sc DE tables. In your script, you used 6 different methods to generate DE tables when the input is bulk RNA-seq data. Whic…
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Hiya,
Can Arriba be used to detect fusions in single-cell RNAseq data (e.g. Smart-seq2). I expect to see a greater number of false positives compared to bulk RNAseq, and with a lower number of read…
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First of all thank you for this nice tool.
I run nebula for differential expression analysis between 2 groups and I realised that my top (by logFC) significant genes are mostly driven by some outlie…
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Hi,
Thank you very much for putting together this code.
I would like to better understand when Bulk2Space might help versus when there are limits to applicability to Bulk2Space, following a jour…
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- [ ] Have a quick start vignette showing some content similar to https://bioconductor.org/packages/release/bioc/vignettes/recount/inst/doc/recount-quickstart.html#2_Quick_start_to_using_to_recount ht…
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I have a workflow question. Here is some background:
I have a Seurat RDS file of integrated ATAC-seq and RNA-seq data from human samples. This data measures TF expression. After running PCA and UMA…
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Hi,
Is it possible to run scFBA without including pooled/bulk RNA-seq data? (Because sometimes this data is not available).
From your README file, it seems that it is possible to run scFBA without…
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In single-cell data, there are a lot of drop-outs, and the fold change may not be calculated (even in bulk-RNA Seq, there are zeros in the wild-type data, so that the fold change could be Infinity). H…
HHHit updated
4 years ago
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Hi,
I have come across the need to analyse GeoMx data that is generated in two different instances. I have successfully run your tool in two separate instances but as these two projects are related…
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Hi @alexdobin
Thanks again for writing & maintaining STAR. The latest diploid mapping feature is very cool. I was wondering how difficult you think it would be to extend it even further, to map to …