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broadinstitute
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epi-SHARE-seq-pipeline
Epigenomics Program pipeline to analyze SHARE-seq data.
MIT License
17
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3
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Filenames
#61
mei-knudson
closed
1 year ago
0
- propagate Seurat params from workflow to task
#60
sidwekhande
closed
1 year ago
1
- Adding count_only flag
#59
mei-knudson
closed
1 year ago
0
- Dynamic memory, adding monitor script
#58
mei-knudson
closed
1 year ago
0
Mei starsolo
#57
mei-knudson
closed
1 year ago
0
Knee plot
#56
mei-knudson
closed
2 years ago
0
- Remove problematic package in archr dockerfile
#55
sidwekhande
closed
2 years ago
0
Knee plot
#54
mei-knudson
closed
2 years ago
0
Knee plot
#53
mei-knudson
closed
2 years ago
0
- Adding sort command to keep QC options consistent
#52
mei-knudson
closed
2 years ago
0
- fixing bugs in the "regular" mode of group_umis; also off by one bug fix for gene in "fast" mode
#51
nchernia
closed
2 years ago
0
- Updating script to handle cases where not all QC outcomes are obse…
#50
mei-knudson
closed
2 years ago
0
Merge joint_cell_calling into main
#49
mei-knudson
closed
2 years ago
0
Barcode plot annotations
#48
mei-knudson
closed
2 years ago
0
Merge insert_size_hist into main
#47
mei-knudson
closed
2 years ago
1
Merge insert_size_hist into main
#46
mei-knudson
closed
2 years ago
0
Minimal inputs
#45
emattei
closed
2 years ago
0
QC metrics in demux
#44
nchernia
opened
2 years ago
2
Update knee/elbow plots to be prettier
#43
nchernia
closed
1 year ago
0
Histogram plot from pdf to png
#42
nchernia
closed
2 years ago
0
Joint QC plot
#41
nchernia
closed
2 years ago
0
- ArchR 'strict' task & Seurat plot changes
#40
sidwekhande
closed
2 years ago
0
Seurat log transform violin plots
#39
sidwekhande
closed
2 years ago
0
run ArchR with lenient and strict parameters
#38
sidwekhande
closed
2 years ago
0
Neva
#37
nchernia
closed
2 years ago
0
Changes to how to call starsolo
#36
nchernia
closed
2 years ago
2
- increase mem for seurat and archr tasks
#35
sidwekhande
closed
2 years ago
0
- Raw and filtered matrices, rds and metadata tsv in seurat and archr tasks
#34
sidwekhande
closed
2 years ago
0
Fixing memory issues in preprocess
#33
nchernia
closed
2 years ago
0
HTML report changes now working
#32
nchernia
closed
2 years ago
0
Revert "List of image files and log files"
#31
emattei
closed
2 years ago
0
List of image files and log files
#30
nchernia
closed
2 years ago
0
HTML report, integer logging, library size plot update
#29
nchernia
closed
2 years ago
1
Merge in changes to log numbers and create html report
#28
nchernia
closed
2 years ago
0
- Notebook plot outputs are now in subwf
#27
sidwekhande
closed
2 years ago
0
Preprocess ONLY
#26
kdong2395
closed
2 years ago
0
Add html report and numbers
#25
nchernia
closed
2 years ago
1
Kdong
#24
kdong2395
closed
2 years ago
1
- Revamped ArchR plots
#23
sidwekhande
closed
2 years ago
0
- Fix filenames for Seurat umaps
#22
sidwekhande
closed
2 years ago
0
- Added new Seurat plots
#21
sidwekhande
closed
2 years ago
0
Dev
#20
sidwekhande
closed
2 years ago
0
merge main into dev
#19
sidwekhande
closed
2 years ago
0
Bug fixes in ArchR logging and subwfs
#18
sidwekhande
closed
2 years ago
0
merging main into sw-tidy-dockerfiles
#17
sidwekhande
closed
2 years ago
0
tidying dockerfiles
#16
sidwekhande
closed
2 years ago
0
dockerfiles to support tools on terra
#15
sidwekhande
closed
2 years ago
0
Dev
#14
sidwekhande
closed
2 years ago
1
- Cloudbuild updated with all the images.
#13
emattei
closed
2 years ago
0
New read names
#12
emattei
closed
2 years ago
0
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