v.1.1 release - Githubissues

ASAP-CRN / harmonized-wf-dev

Repo for testing and developing a common postmortem-derived brain sequencing (PMDBS) workflow harmonized across ASAP

Apache License 2.0

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v.1.1 release #57

Open ergonyc opened 1 month ago

ergonyc commented 1 month ago

For the August release of ASAP CRN datasets several small updates have been made to the PMBDS workflows.

IMPLIMENTED

[x] data manifest updates: Pull Req #54
[x] data integrity testing updates: Pull Request #56

WIP

[ ] CellAssign training parameter updates
[ ] cell_type taxonomy references
[ ] "flavors" of QC metrics for SC vs SN, and ASSAY specific

FUTURE

[ ] CellRanger QC metrics added to metadata
[ ] CellBender QC metrics added to metadata
[ ] add post-preprocessing metadata and adata artifact archived in "cohort_analysis" collection
[ ] update python env to 3.12
[ ] update scvi-tools to v1.15

ergonyc commented 1 month ago

We ought to compile the CellRanger QC metrics into tabular form and pass along as part of the metadata. Potentially also some of the auxilary CellBender metrics.

TODO: enumerate which metrics

ergonyc commented 1 month ago

I think we need to add a "pre-filtered" summary of metadata and possibly an unfiltered "merged" adata object. i.e the output of plot_qc_metrics.py. That will offer users an easy entry point for alternative processing / filtering. e.g. if the user wanted to develop an "atlas" of cells / cell-types for a specific brain region, they would harmonize a subset of the overall cohort.

ergonyc commented 1 month ago

We should also upate scvi-tools to v1.15 and python to 3.12 at some point. Maybe after the next release... maybe with the other updates / testing

ergonyc commented 1 month ago

There's a subtle bug in the cellassign code which estimates the library size parameter after subsetting to the marker genes. This should be calculated before subsetting.