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34 Open 154 Closed
34 Open 154 Closed
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Issues list

Gene cross-checking component
#834 opened Jul 10, 2024 by jakubmajercik
@jakubmajercik
scGPT: use sparse matrix calculations
#790 opened Apr 19, 2024 by dorien-er
Adding an integration test for scGPT integration workflow
#784 opened Apr 11, 2024 by dorien-er
@jakubmajercik
Generate scGPT preproc subworkflow
#782 opened Apr 4, 2024 by dorien-er
Generate scGPT utils
#781 opened Apr 4, 2024 by dorien-er
implement scGPT cell type annotation workflow
#777 opened Apr 2, 2024 by jakubmajercik
1
@jakubmajercik
Create mudata namespace an move components that perform basic operation on the mudata objec to it (delete_layer, remove_modality). Most of these currently are put in the metadata or filter namespace.
#770 opened Mar 26, 2024 by DriesSchaumont
TODO list for the paper
#738 opened Mar 8, 2024 by VladimirShitov
8 tasks
1
Update scarches component
#709 opened Feb 15, 2024 by VladimirShitov
@VladimirShitov
FEATURE: Add functionality to exlcude some features from the analysis.
#696 opened Feb 7, 2024 by DriesSchaumont
Add more per-component logging
#649 opened Jan 12, 2024 by DriesSchaumont
Capitalized modality names are not processed by full pipeline workflow enhancement New feature or request
#626 opened Dec 5, 2023 by KaiWaldrant
3
Multi sample test files for ATAC components
#625 opened Nov 28, 2023 by VladimirShitov
Remove big binary files
#622 opened Nov 24, 2023 by rcannood
2
cellbender output saved in additional layer enhancement New feature or request
#618 opened Nov 16, 2023 by magochab
1
Provide a clearer error message when the column provided to var_gene_names does not exist. enhancement New feature or request
#617 opened Nov 15, 2023 by DriesSchaumont
Report the number/percentage of HVGs present in 2 modalities
#608 opened Oct 31, 2023 by VladimirShitov
Output the number of highly variable genes selected enhancement New feature or request
#595 opened Oct 24, 2023 by ddemaeyer
1
Add scarches workflow
#582 opened Oct 6, 2023 by DriesSchaumont
set default values of output files in workflows
#550 opened Sep 11, 2023 by rcannood
Refactor the TotalVI component to also allow running without reference
#546 opened Sep 8, 2023 by ddemaeyer
5
Redundancy in label transfer components?
#539 opened Sep 6, 2023 by VladimirShitov
1
Rethink documentation organisation.
#517 opened Aug 18, 2023 by DriesSchaumont
Create gatekeeper components to perform checks in a pipeline
#435 opened Jun 14, 2023 by DriesSchaumont
Move common code to a separate script
#413 opened Jun 5, 2023 by VladimirShitov
4 tasks
1
ProTip! Updated in the last three days: updated:>2024-11-04.