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nf-core
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scdownstream
A single cell transcriptomics pipeline for QC, integration and making the data presentable
https://nf-co.re/scdownstream
MIT License
43
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12
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Add support for rapids-singlecell
#80
nictru
closed
2 months ago
1
Implement reference mapping
#79
nictru
closed
2 months ago
1
Implement gpu support for relevant tools
#78
nictru
closed
2 months ago
1
Use nf-core cellbender module instead of local module
#77
nictru
closed
3 months ago
1
fix merge.py
#76
fbnrst
closed
3 months ago
1
additional output for cellbender
#75
fbnrst
closed
3 months ago
1
fix gene symbols in celltypist
#74
fbnrst
closed
3 months ago
2
Add support for gene symbols specified in columns other than the var.index
#73
nictru
closed
3 months ago
7
celltypist fails with value error
#72
fbnrst
closed
3 months ago
1
Improve output structure and docs
#71
nictru
closed
3 months ago
1
Implement integration HVG selection
#70
nictru
closed
4 months ago
1
Implement GPU support for relevant tools
#69
nictru
closed
2 months ago
4
Fix doublet filtering out non-doublets cells
#68
nicoaira
closed
4 months ago
6
docs: skeleton for guiding users towards interpretation
#67
smoe
closed
3 months ago
7
Fix cellbender ch_raw reference
#66
nictru
closed
4 months ago
1
AMBIENT_RNA_REMOVAL needs revision - runtime error ch_raw undefined with cellbender
#65
smoe
closed
4 months ago
0
Minimal sample sheet with both filtered and unfiltered produced by scrnaseq triggers celda decontx runtime error
#64
smoe
closed
2 months ago
2
Update schema_input.json: require filtered or unfiltered
#63
smoe
closed
4 months ago
3
Implement automatic filtering if only unfiltered matrix is available
#62
nictru
closed
4 months ago
2
Add parameter for aggregation of duplicate var names
#61
nictru
closed
4 months ago
1
Add support for background matrix in decontX
#60
nictru
closed
4 months ago
1
docs: describing sources of input and interaction with workflow parameters
#59
smoe
closed
4 months ago
5
cellbender -> pytorch -> disk full, but it is not!
#58
smoe
closed
4 months ago
3
Add support for background matrix in `decontX`
#57
nictru
closed
4 months ago
0
Allow skip of ambient_removal by introducing method 'none'
#56
smoe
closed
4 months ago
5
Use raw cellranger outputs for cellbender
#55
nictru
closed
4 months ago
3
Add support for h5 input format
#54
nictru
closed
5 months ago
1
cellbender needs raw count matrix as input
#53
fbnrst
closed
4 months ago
0
48 add support for h5 input format
#52
fbnrst
closed
5 months ago
1
CELDA_DECONTX - bails out over negative size factors
#51
smoe
closed
4 months ago
13
Fix singularity cache problems
#50
nictru
closed
5 months ago
1
MPLCONFIGDIR expected in $HOME outside what singularity allows
#49
smoe
closed
5 months ago
2
Add support for h5 input format
#48
nictru
closed
5 months ago
1
Update docs
#47
nictru
closed
5 months ago
1
Add citations
#46
nictru
closed
5 months ago
1
Implement custom filtering
#45
nictru
closed
5 months ago
1
Implement singleR celltype annotation
#44
nictru
opened
5 months ago
2
Update documentation of supported ambient RNA removal methods
#43
nictru
closed
5 months ago
1
Implement celltypist cell type assignment
#42
nictru
closed
5 months ago
1
Implement scar ambient rna removal
#41
nictru
closed
5 months ago
1
Implement soupx ambient rna removal
#40
nictru
closed
5 months ago
1
Implement cellbender ambient rna removal
#39
nictru
closed
5 months ago
1
Implement scds doublet detection
#38
nictru
closed
5 months ago
1
Implement doubletdetection doublet detection
#37
nictru
closed
5 months ago
1
Implement scrublet doublet detection
#36
nictru
closed
5 months ago
1
Implement seurat integration
#35
nictru
closed
5 months ago
1
Implement combat integration
#34
nictru
closed
5 months ago
1
Implement bbknn integration
#33
nictru
closed
5 months ago
1
Implement harmony integration
#32
nictru
closed
5 months ago
1
Implement scAR ambient RNA removal
#31
nictru
closed
5 months ago
2
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