Guillaume Poirier-Morency

Assign cells to coarse cell types when creating pseudo-bulks

2

Once cells are assigned to URIs from the [cell ontology](https://cell-ontology.github.io/), it might be necessary in some case to aggregate at a more coarse level to get enough depth per pseudo-bulk....

Handle MEX datasets with barcode_metadata.tsv.gz files

1

This file format is used for datasets that are aligned against a combined reference (i.e. hg19 + mm10). It contains additional columns with per-species counts and a call that indicate...

Tools from NCBI and the RNA-Seq pipeline obtain the API key from this environment variable. It should be used if no value is set in Gemma.properties.

I've tried every variant, they all crash. Retrace is available here: https://retrace.fedoraproject.org/faf/reports/1016794/

On Linux and Mac, it's better to expect dot to be in the path since all the offered installation options would result in that being the case. On Windows, the...

- [ ] detect platforms/datasets that are suitable for Cell Ranger - [ ] add a task for generating the reference (optional, we can use those provided by Cell Ranger)...

The workaround is to invoke `package` which builds the test JAR first and then make it resolvable for other dependencies. Maven actually recommend using a separate project for sharing test...

Filtering genes suitable for DEA should not use values adjusted for library size

4

The filtering that we do for DEA is very minimal and stringent and aim mainly at excluding repetitive values. We exclude: - genes that have a variance of less than...