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broadinstitute
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epi-SHARE-seq-pipeline
Epigenomics Program pipeline to analyze SHARE-seq data.
MIT License
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Pass the --soloFeatures in input
#111
emattei
closed
1 year ago
1
Gene names
#110
mei-knudson
closed
1 year ago
0
Gene names
#109
mei-knudson
closed
1 year ago
0
no way to force exit jupyter nb execution via papermill
#108
sidwekhande
closed
1 year ago
2
Create seqspec for the fastq that we will generate
#107
emattei
closed
1 year ago
2
- Changing read structure determination; increasing memory; adding m…
#106
mei-knudson
closed
1 year ago
0
Main rebase
#105
emattei
closed
1 year ago
0
- Update %mt in seurat task
#104
sidwekhande
closed
1 year ago
0
- Applying Sid changes.
#103
emattei
closed
1 year ago
0
Update %mt default in seurat task
#102
sidwekhande
closed
1 year ago
0
Count matrix with gene names wrong
#101
emattei
closed
1 year ago
1
Change MITO fraction
#100
emattei
closed
1 year ago
0
ddqc
#99
sidwekhande
opened
1 year ago
0
Dropulation
#98
emattei
closed
1 year ago
1
Requester pay google bucket
#97
emattei
opened
1 year ago
0
Using method in Juliana's paper identify variable genes
#96
emattei
opened
1 year ago
0
FastqQC in the pipeline?
#95
emattei
opened
1 year ago
0
Version 5 Seurat
#94
emattei
opened
1 year ago
4
Extra task to localize inputs for not Terra usage
#93
emattei
opened
1 year ago
1
Matrices merging
#92
emattei
opened
1 year ago
0
Joint QC analysis
#91
emattei
opened
1 year ago
0
DORCs refactoring
#90
emattei
opened
1 year ago
0
clump removal/doublets
#89
emattei
opened
1 year ago
0
Cell type annotation
#88
emattei
opened
1 year ago
0
Make new raw fastqs
#87
emattei
closed
1 year ago
1
Ambient RNA
#86
emattei
opened
1 year ago
0
New IGVF transcriptome reference
#85
emattei
closed
1 year ago
11
Merge sw-default-changes to main
#84
sidwekhande
closed
1 year ago
0
Potential version 1
#83
emattei
closed
1 year ago
2
WorkflowManagerActor: Workflow f5905e43-a5fe-423c-be74-3afbfc0d5540 failed
#82
khsjh
closed
1 year ago
1
Pkr input
#81
emattei
closed
1 year ago
0
Atac refactoring qc plots
#80
mei-knudson
closed
1 year ago
0
Plot all quadrants of density plot
#79
mei-knudson
opened
1 year ago
0
Trim fastqs atac
#78
emattei
closed
1 year ago
0
Updates from Kevin
#77
nchernia
closed
1 year ago
0
Various plot fixes in ArchR and Seurat task
#76
sidwekhande
closed
1 year ago
0
- Updating density plotting to handle case where no cells pass both …
#75
mei-knudson
closed
1 year ago
0
Fix joint density
#74
mei-knudson
closed
1 year ago
0
Make html even more beautiful with interactive plotting
#73
nchernia
opened
1 year ago
0
Make html beautiful with tabs
#72
nchernia
opened
1 year ago
0
Fix the ATAC log plot
#71
nchernia
closed
1 year ago
0
UMAP percent mito colored same color scheme as nUMI and nGene
#70
nchernia
opened
1 year ago
0
bigger labels on seurat plots
#69
nchernia
closed
1 year ago
0
Remove dots from violin plot
#68
nchernia
closed
1 year ago
0
Color genes by nUMI plot by percent mito
#67
nchernia
opened
1 year ago
0
Labels bigger on joint cell calling plot
#66
nchernia
opened
1 year ago
0
Add commas in html report
#65
nchernia
opened
1 year ago
0
Kdong
#64
kdong2395
closed
1 year ago
0
10X rna
#63
mei-knudson
closed
1 year ago
0
Fix qc rna
#62
mei-knudson
closed
1 year ago
0
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