Jeremy Simon
Jeremy Simon
Hi @haowenz, I tend to not force use of the 10X barcode include-list since it is possible there could be valuable information/real cells, but I noticed that some scATACseq data...
Hi @kaizhang - This is mainly a request for more documentation, as I didn't see this explicitly mentioned anywhere (though perhaps I missed it) but is likely useful to others....
Hey @ncborcherding - I have a dataset where there are 3 sample groupings that I'd like to compare. Is it possible to implement something in `splitEnrichment` that allows for >2...
### Description of the bug I have an experimental setup with biological triplicates of my conditions: `treated_5hr`, `treated_7hr`, and `control`. My sample names as specified in the samplesheet look like...
### Description of feature Maybe this isn't the typical case for most users, but my experiment has multiple replicates of treatment and control. If I wanted to check how concordant...
### Description of feature I've read the `crisprseq` and `MAGeCK` documentation a few times and the description and function of the `day0_label` is still a bit unclear to me, both...
Hi @ncborcherding I'm wondering if it's at all possible to include another option in `cloneCall` to be CDR3 AA + V + J, which would more closely match `immunarch`'s `TrackClonotypes(aa+v+j)`...
Hi - it seems MSigDB has a new update for 2024 (mouse and human) and one of the big changes/additions is the KEGG MEDICUS collection (original KEGG pathways seem to...
Hi, I'm just curious if it is theoretically possible to detect reads consisting of inter- or intra-chromosomal translocations with chromap? Or would this only be possible with a more traditional...
### Description of feature Currently, there doesn't seem to be a way to specify all the 10x read chemistries supported by `simpleaf` here: https://github.com/COMBINE-lab/simpleaf/blob/main/resources/chemistries.json In particular, I'd like to run...