ASAP-CRN pmdbs-sc-rnaseq-wf issues

ASAP-CRN / pmdbs-sc-rnaseq-wf

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

Apache License 2.0

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issues

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tested changes

#77 ergonyc closed 4 days ago
0
prettify scripts with functions and __name__=__main__

#76 ergonyc closed 4 days ago
0
update wdl and

#75 ergonyc closed 4 days ago
0
update python scripts

#74 ergonyc opened 5 days ago
1
scib-metrics report not exported?

#73 ergonyc opened 5 days ago
1
pre- and post- filtering metadata capture

#72 ergonyc opened 5 days ago
1
update to clustering_umap.py to curate additional leiden clusters at multiple resolutions.

#71 ergonyc opened 5 days ago
1
Do we do "batch" correction sample-wise or batch-wise?

#70 ergonyc opened 5 days ago
2
rename scripts to clarify their function/role

#69 ergonyc opened 5 days ago
1
make final artifact name: "final"

#68 ergonyc opened 5 days ago
0
make "Fixed" parameters for each script clear

#67 ergonyc opened 5 days ago
0
"project" is NOT an ASAP_CRN defined value. -> "team", "dataset"

#66 ergonyc opened 5 days ago
1
Feature/bucket restructure

#65 kfang4 closed 5 days ago
1
scRNAseq "flavors", technology and sc vs sn

#64 ergonyc opened 2 weeks ago
0
Depricate CellTyping? is under-constrained

#63 ergonyc opened 4 weeks ago
1
CellAssign training parameter updates

#62 ergonyc opened 1 month ago
0
update python env to 3.12

#61 ergonyc opened 1 month ago
0
update scvi-tools to v1.2

#60 ergonyc opened 1 month ago
0
Use wf-common submodule

#59 kfang4 closed 2 months ago
0
Add tool and library versions in README

#58 kfang4 closed 3 months ago
0
v.1.1 release

#57 ergonyc opened 3 months ago
7
Feature/data integrity test

#56 kfang4 closed 2 months ago
3
Update workflow for v1.0.0 release

#55 ergonyc opened 4 months ago
1
Feature/update manifest

#54 kfang4 closed 4 days ago
4
Feature/wdl ci

#53 kfang4 closed 4 months ago
0
Output the scib results SVG

#52 kfang4 closed 4 months ago
1
update workflow_diagram

#51 ergonyc closed 5 months ago
2
Remove old PDFs

#50 kfang4 closed 5 months ago
0
old .pdf files for data dictionary file manifest

#49 ergonyc closed 5 months ago
1
fix scib_report export bug

#48 kfang4 closed 5 months ago
0
Develop

#47 kfang4 closed 5 months ago
0
Upldate WDL to impliment the simple CI functions

#46 ergonyc closed 5 months ago
0
Scib artifact metrics

#45 ergonyc closed 5 months ago
0
add UMAP 1+2 to exported metadata

#44 ergonyc closed 5 months ago
0
UMAPs needed in metadata

#43 ergonyc closed 5 months ago
1
Add UMAP to metadata export

#42 ergonyc closed 6 months ago
1
Feature/unembargoed scherzer

#41 kfang4 closed 6 months ago
0
Feature/staging buckets

#40 kfang4 closed 7 months ago
0
Feature/reduce storage

#39 kfang4 closed 7 months ago
0
Develop

#38 kfang4 closed 8 months ago
0
Feature/optimization

#37 kfang4 closed 8 months ago
0
Feature/update promote staging data script

#36 kfang4 closed 8 months ago
0
Feature/test full cohort

#35 kfang4 closed 8 months ago
0
Feature/test python wf

#34 kfang4 closed 8 months ago
0
Chore/update docs

#33 kfang4 closed 8 months ago
0
Feature/ah test

#32 ergonyc closed 9 months ago
0
scvi-tools 1.1.0

#31 ergonyc closed 8 months ago
1
Scanpy implementation

#30 kfang4 closed 9 months ago
0
add resources, process.py clarify

#29 ergonyc closed 9 months ago
0
Annot stub

#28 ergonyc closed 9 months ago
0