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The cutoffs for defining background droplets were based on the DSB tutorial suggestions. I recently examined the ADT distributions for many tissue libraries and found that a small number of libraries …
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Hi, I'd like to try this tool out but am wondering how to format the infernal, cove, or text files properly. It appears that at one point there may have been an Appendix section in the readme, but I'm…
byee4 updated
2 months ago
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```sh
R
```
```
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and…
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Hello,
I am trying to run decoupleR but have just encountered an error after updating to the most recent version today when using run_ulm or run_mlm:
```R
sample_acts
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In the text there it writes:
> For example, the codon TCA (or UGA if we describe it as an RNA sequence) codes for S, the amino acid Serine.
Should that be `UCA` for the RNA sequence?
(I wa…
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Hi!
I have rRNA depleted total RNA-Seq reads obtained using below kits. Can I use these to identify all AS events? (I am getting SEs and MXEs and no other as events using rMATS.) Is there any speci…
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- [48d354f5-a5ca-4f35-a3bb-fa3687502252](https://cellxgene.cziscience.com/collections/48d354f5-a5ca-4f35-a3bb-fa3687502252)
- obs.var_time:P7 - update to 7 day [MmusDv:0000117]
- [d86517f0-fa7e-4…
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RiboViz (v.1.1.0 I think) is currently not generating gene counts & TPMs (SAMPLE_tpms.tsv) for some datasets when yaml flag rpf is FALSE.
The problem must be in scripts/generate_stats_figs.R becaus…
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Hi,
I'm trying to reuse some relatively "old" illumina RNA-seq data not strand-specific. What would be the best way to process them?
Thanks a lot
Francesco
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I have been looking into using the RNA-seq data but have some questions on the gene annotations for the V2-RNA-seq data that I get from running your GDC-prepare-function.
How do the 21022 genes tha…