Alexei Martsinkovskiy
Alexei Martsinkovskiy
The example for creating a SCope compatible loom file calls an objects metadata. However, the loomfile, at least as it is outputed by PySCENIC, seems to contain no metadata field.
When running on a broadpeak file, callvar does the following: ``` macs3 callvar -b Met.mRp.clN_peaks.broadPeak -t ~/results/chromap/merged_replicate/met_filtered.bam --outdir results/var -o variants.vcf ``` File "MACS3/Signal/RACollection.pyx", line 358, in MACS3.Signal.RACollection.RACollection.get_PosReadsInfo_ref_pos File "MACS3/Signal/RACollection.pyx",...
**Describe the bug** It seems that the MD tag generated in Chromap sometimes can incorrectly begin with a letter. It seems this behavior, to my understanding occurs when the first...
### Description of the bug some of the docker containers used in the pipeline are in old deprecated docker formats, and docker doesn't want to pull them: ### Command used...
### Checklist - [X] I added a descriptive title - [X] I searched open reports and couldn't find a duplicate ### What happened? It outputs the titled error when I...
Hi all, Loving the tool and have been playing around with it. I haven't delved too far into the gsVA/ssGSEA code, so that might be addressed there. Feel free to...
Hi all, So I wanted to run cellchat per biological replicate. Mainly, it's because I am concerned that for some population, it can be defined as interacting even though cells...
Hi all, Is there any suggestion/best practices on whether one should or should not use orphan recovery? My feeling is that it should be used in cases where the library...
I know this is an open issue, but I also wanted to ask if there is some possible citation to cite? I like the tool, and it would be nice...
Hi all, There is a package called collapse that implements fast quantile calculations, and the backend is written in C++. It is much faster than the base quantile function in...