issues
search
AlexsLemonade
/
scpca-nf
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
BSD 3-Clause "New" or "Revised" License
12
stars
2
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Fix merge report bugs related to multiplexing
#697
sjspielman
closed
8 months ago
0
Skip any additional processing to processed objects with 0 cells
#696
allyhawkins
closed
8 months ago
2
Add precommit ci to CONTRIBUTING.md
#695
sjspielman
closed
8 months ago
2
add autofix setting & update
#694
jashapiro
closed
8 months ago
3
add some pre-commit.ci options
#693
jashapiro
closed
8 months ago
0
Add docs for custom cell type references
#692
sjspielman
closed
8 months ago
2
Standardize celltype report filenames
#691
arkid15r
closed
9 months ago
1
Add troubleshooting section to external instructions
#690
sjspielman
opened
9 months ago
3
QC report aesthetic updates
#689
sjspielman
closed
9 months ago
1
Add merge.nf external instructions
#688
sjspielman
closed
9 months ago
7
Add cellassign note to QC if not run
#687
sjspielman
closed
9 months ago
6
Merge main code into development
#686
sjspielman
closed
9 months ago
0
Remove duplicated code in cell type module
#685
sjspielman
closed
9 months ago
0
ADT filtering information not provided in AnnData CITE objects
#684
sjspielman
closed
9 months ago
1
Update merged object for anndata export
#683
sjspielman
closed
9 months ago
0
Deal with libraries that don't have any cells after removing empty droplets
#682
allyhawkins
closed
6 months ago
1
Missing information in merged AnnData objects
#681
sjspielman
closed
9 months ago
16
Prep for v0.7.2
#680
allyhawkins
closed
9 months ago
3
Rename spatial report with dash
#679
sjspielman
closed
9 months ago
0
Update spatial report name
#678
sjspielman
closed
9 months ago
1
Update sample_type printing logic to handle multiplex samples
#677
sjspielman
closed
9 months ago
1
Account for multiplex libraries when printing sample_type info box
#676
sjspielman
closed
9 months ago
1
Remove any unused cell hash oligos from unfiltered and fix conversion issue
#675
allyhawkins
closed
9 months ago
7
Check for missing bulk in genetic demux
#674
jashapiro
opened
9 months ago
0
Account for missing inputs everywhere
#673
jashapiro
closed
9 months ago
1
Add missing_inputs branches to non-alevin mapping
#672
jashapiro
closed
8 months ago
1
Fix missing files directory bug
#671
sjspielman
closed
9 months ago
0
Fix bug in files_directory checking
#670
sjspielman
closed
9 months ago
2
Prepare for scpca-nf release v0.7.2
#669
allyhawkins
closed
9 months ago
2
Check that all column names are "barcode"
#668
allyhawkins
closed
9 months ago
1
Add sample type to metadata and associated QC box
#667
sjspielman
closed
9 months ago
0
Update colData merging based on altExps 😈
#666
sjspielman
closed
9 months ago
7
Actually remove unclassified cells from heatmap
#665
allyhawkins
closed
9 months ago
5
Skip sample metadata addition to colData if cellhash is present
#664
allyhawkins
closed
9 months ago
1
Maybe add a note to QC report about when skipping CellAssign
#663
allyhawkins
closed
9 months ago
2
Deal with small numbers of cells and CellAssign
#662
allyhawkins
closed
9 months ago
5
Retain adt colData columns when merging, and keep cellhash main colData
#661
sjspielman
closed
9 months ago
1
Fix merge.nf workflow adt and multiplex check
#660
sjspielman
closed
9 months ago
4
Don't rename rowdata `gene_ids` column
#659
sjspielman
closed
9 months ago
1
Retain filter columns when merging
#658
sjspielman
closed
9 months ago
0
Remove cluster metadata from SCE before merging
#657
sjspielman
closed
9 months ago
3
Keep cell type columns when merging
#656
sjspielman
closed
9 months ago
1
Keep cell type annotation coldata in the merge workflow
#655
sjspielman
closed
9 months ago
1
Prepare for scpca-nf release v0.8.0
#654
allyhawkins
closed
7 months ago
2
Update qc report names
#653
sjspielman
closed
9 months ago
1
Fix merge script join bug
#652
sjspielman
closed
9 months ago
11
Make sure dimensions for UMAPs exist
#651
allyhawkins
closed
9 months ago
1
Render celltype report only if library is not a cell line
#650
sjspielman
closed
9 months ago
5
Fail for missing mapping files, and other missing files
#649
sjspielman
closed
9 months ago
0
Skip cell lines when cell typing
#648
sjspielman
closed
9 months ago
1
Previous
Next