Guillaume Poirier-Morency

When splitting an experiment, there's a chance that the resulting splits will contain less than 4 samples like it's the case for GSE270175. The exception should be raised only if...

NullPointerException in ExpressionExperimentController.loadExpressionExperimentDetails() DWR call

1

 Related to #1206

Handle datasets with MEX data at both sample and series-level

1

This is tricky, because we merge supplementary materials from both levels, so in this particular case, the files should not be merged. Example: GSE208742

The strategy that I've implemented is to map single cell data vectors to elements of a platform using various IDs with some predefined precedence: - composite sequence name - NCBI...

Test cases for single cell data loading

1

The @PavlidisLab/curation team compiled a list of single-cell experiments that need special treatment on import. We can convert those into test cases. ## Bulk/single-cell mix Contains a mixture of bulk...

Support 10x clusters format

1

This is very low priority. It appears that the clustering is done per-sample, so there would be no shared cell types across samples. Reference: https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-secondary-analysis

This is supported by baseCode without downtime, so there's no reason we don't refresh them regularly at runtime or have some mechanism for reloading them. - [ ] add a...

This came to my attention because I noticed that Uberon has mouse and human subsets. This would have two main benefits by preventing irrelevant terms showing up in curation tools...

https://j-a-w-r.github.io/integration/spring.html

Support reading cell IDs from MEX datasets with cells.tsv.gz

1

I've seen it a couple of times. It needs more investigation. Example Example from GSM7431296 bc_wells | sample | species | gene_count | tscp_count | mread_count | bc1_well | bc2_well...