Christopher Andrew Mancuso

OWL files seem empty so can't convert to OBO

9

We are going to start doing some work in our group comparing transcriptome samples across a number of species. It looks like the upheno ontology is exactly what we are...

allow use of .gz when specifying fast and gtf

4

### Description of feature I was trying to run the scrnaseq pipeline specifying a fasta and gtf file. I downloaded from ensembl but they were gunzipped. I searched Slack and...

In `_get_negatives` it would be good to display what genes were considered neutrals. Possibly even which Term ID they came from and could add the neutral marker in addition to...

@billspat @jacobnewsted It might be good to have one/all of the following displayed when the validation is run, which can be taken care of in the python package 1. have...

Add a function so a user can aggregate results across different models - Does it make sense to do across different gene sets? - How to handle going across different...

Currently, to make output edgelist of the top genes, it needs to read/parse the whole edgelist. Some quick thoughts - Save edgelist files as json with node as key and...

In the web server paper review and from talking to other people, I have heard people would like more guidance on which network to choose. Since the performance of the...

change example and defaults

3

change the example and defaults to match PCD example on web server

Trimming R1 fast files in all aligners

4

### Description of feature I'm following up on a slack post that I put out 2 months ago at https://nfcore.slack.com/archives/CHN5BV5DW/p1712178056321859 I had a question about the fastq format needed for...

Reproducibility and Documentation

1

- fix the unit tests - add good example gene sets - update all documentation, can two versions of documentation be up on ReadtheDocs - check all examples run, including...