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hubmapconsortium
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sc-atac-seq-pipeline
ATAC-seq pipelines for HuBMAP
MIT License
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4
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Renaming boolean to avoid rebinding function name
#68
SFD5311
closed
6 days ago
0
Move writing the cell_col_data_df
#67
pennycuda
closed
3 weeks ago
0
Remove cells without cluster assignments from ArchR
#66
pennycuda
closed
1 month ago
0
Drop nuclei without cluster assignments
#65
pennycuda
closed
1 month ago
0
Exposing peaks files and qc measures as pipeline outputs
#64
SFD5311
closed
2 months ago
0
Updating docker_images.txt
#63
SFD5311
closed
2 months ago
0
Reintroducing metadata file argument to CWL steps
#62
SFD5311
closed
3 months ago
0
Sfd5311/repo refactor
#61
SFD5311
opened
5 months ago
0
Refactor sc-atac-seq-pipeline repository
#60
SFD5311
opened
5 months ago
0
2 Motif Analysis CWL Steps, Neither Used?
#59
SFD5311
opened
5 months ago
0
Allow for multiple orig_dir
#58
seschultz
closed
5 months ago
0
change default barcode slice for multiome
#57
seschultz
opened
6 months ago
0
Split ArchR into two steps
#56
pennycuda
closed
5 months ago
0
Split ArchR analysis into 2 steps
#55
pennycuda
closed
6 months ago
0
Bumping MACS version
#54
SFD5311
closed
10 months ago
0
Fixes to bulk pipeline
#53
SFD5311
closed
10 months ago
0
Sfd5311/update bulk cwl steps
#52
SFD5311
closed
10 months ago
0
Marking pipeline outputs as data products
#51
SFD5311
closed
1 year ago
0
Add is_data_product field to pipeline manifest
#50
SFD5311
closed
5 months ago
0
Empty frags files in sciATAC and snareseq data
#49
SFD5311
opened
1 year ago
0
Split `run_ArchR_analysis.R` for multiome processing
#48
mruffalo
opened
1 year ago
0
Improve reporting of too few cells passing filtering criteria
#47
mruffalo
opened
2 years ago
0
Better error message for few cells, formatting changes, and fix to ArchR commit
#46
wshands
closed
2 years ago
0
Update `sc_atac_seq_prep_process_analyze.cwl` to provide expected outputs
#45
mccalluc
opened
2 years ago
0
Write anonymized BAM file with BAMboozle tool
#44
mruffalo
opened
2 years ago
0
Write genome build and other annotations as machine-readable outputs to each pipeline run
#43
mruffalo
opened
2 years ago
0
Matrix decomposition failure in smoothing cell-by-gene matrix
#42
mruffalo
opened
2 years ago
0
Failure in computing Jaccard similarity matrix when too many cells
#41
mruffalo
opened
3 years ago
0
add initial code to dockerize archr
#40
wshands
closed
2 years ago
0
Sfd5311/fix bulk qc
#39
SFD5311
closed
3 years ago
0
Tweak parameters (filtering, bin size, etc.) for Stanford snATAC-seq processing
#38
mruffalo
opened
3 years ago
0
Support Dockstore GitHub apps feature
#37
wshands
closed
3 years ago
0
Sfd5311/add bulk pipeline manifest
#36
SFD5311
closed
3 years ago
1
Failure to write cell-by-gene matrix as HDF5
#35
mruffalo
closed
3 years ago
1
Add pipeline option to omit BAM file
#34
mruffalo
closed
3 years ago
2
Save cell by gene matrix before smoothing also
#33
mruffalo
closed
3 years ago
1
Save/convert anything appropriate in H5AD format
#32
mruffalo
closed
3 years ago
1
consolidate assay processing
#31
wshands
closed
3 years ago
0
Consolidate assay specific processing
#30
wshands
closed
3 years ago
1
Add tk to avoid error when installing R packages
#29
wshands
closed
3 years ago
0
Rebuild Docker image on newest version of R base image
#28
mruffalo
closed
3 years ago
0
Do not generate/pass protected data in pipeline
#27
pdblood
closed
3 years ago
1
surface bin sizes input
#26
wshands
closed
4 years ago
0
add bins of size 50 and 1000
#25
wshands
closed
4 years ago
0
switch to https://schema.org/version/latest/schema.rdf
#24
mr-c
opened
4 years ago
1
Reduce default minimum bin size to 50
#23
mruffalo
closed
3 years ago
0
fix so test sample will pass peak analysis
#22
wshands
closed
4 years ago
0
Report alignment QC metrics
#21
mruffalo
closed
3 years ago
1
Optimize scatter by calling downstream analysis from snap file creation code
#20
wshands
closed
4 years ago
0
Enhance the documentation in the README.md
#19
wshands
closed
4 years ago
0
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