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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
30
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7
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Add preprocess_only parameter
#100
nictru
closed
2 days ago
1
Add label specific UMAP and clustering option
#99
nictru
closed
1 week ago
1
Add support to Celltypist for non-human species.
#98
tbrittoborges
closed
1 week ago
0
Add MT percentage filtering
#97
tbrittoborges
closed
1 week ago
4
Allow using reference model without base adata
#96
nictru
closed
2 weeks ago
1
Add support for learning an scANVI model based on a given scVI model and cell type annotations
#95
nictru
closed
2 weeks ago
0
Fix problems with `counts` layer references
#94
nictru
closed
2 weeks ago
1
Add support for rank_genes_groups
#93
nictru
closed
2 weeks ago
1
Add PAGA calculation and improve reporting
#92
nictru
closed
2 weeks ago
1
Counts layer required for Scds and Solo is missing
#91
pakiessling
closed
2 weeks ago
0
Pipeline not running correctly on GPU
#90
pakiessling
closed
2 weeks ago
5
Fix `meta.expected_cells` not passing to commnad call (#88)
#89
tbrittoborges
closed
3 weeks ago
1
Add option for per-sample specification of doublet detection thresholds
#88
nictru
opened
3 weeks ago
0
Add MT percentage filtering
#87
nictru
closed
1 week ago
0
Fix cellbender dependency problem
#86
nictru
closed
3 weeks ago
1
Add support for cellbender expected cells
#85
nictru
closed
3 weeks ago
1
Implement meta.expected_cells (cellbender)
#84
tbrittoborges
closed
3 weeks ago
1
MultiQC fails with latest dev release
#83
alexblaessle
opened
4 weeks ago
0
Add rapids implementations for more tools
#82
nictru
closed
1 month ago
1
Add sample size table
#81
nictru
closed
1 month ago
1
Add support for rapids-singlecell
#80
nictru
closed
1 month ago
1
Implement reference mapping
#79
nictru
closed
1 month ago
1
Implement gpu support for relevant tools
#78
nictru
closed
1 month ago
1
Use nf-core cellbender module instead of local module
#77
nictru
closed
1 month ago
1
fix merge.py
#76
fbnrst
closed
1 month ago
1
additional output for cellbender
#75
fbnrst
closed
1 month ago
1
fix gene symbols in celltypist
#74
fbnrst
closed
1 month ago
2
Add support for gene symbols specified in columns other than the var.index
#73
nictru
closed
1 month ago
7
celltypist fails with value error
#72
fbnrst
closed
1 month ago
1
Improve output structure and docs
#71
nictru
closed
2 months ago
1
Implement integration HVG selection
#70
nictru
closed
2 months ago
1
Implement GPU support for relevant tools
#69
nictru
closed
1 month ago
4
Fix doublet filtering out non-doublets cells
#68
nicoaira
closed
2 months ago
6
docs: skeleton for guiding users towards interpretation
#67
smoe
closed
2 months ago
7
Fix cellbender ch_raw reference
#66
nictru
closed
2 months ago
1
AMBIENT_RNA_REMOVAL needs revision - runtime error ch_raw undefined with cellbender
#65
smoe
closed
2 months ago
0
Minimal sample sheet with both filtered and unfiltered produced by scrnaseq triggers celda decontx runtime error
#64
smoe
closed
1 month ago
2
Update schema_input.json: require filtered or unfiltered
#63
smoe
closed
2 months ago
3
Implement automatic filtering if only unfiltered matrix is available
#62
nictru
closed
2 months ago
2
Add parameter for aggregation of duplicate var names
#61
nictru
closed
2 months ago
1
Add support for background matrix in decontX
#60
nictru
closed
3 months ago
1
docs: describing sources of input and interaction with workflow parameters
#59
smoe
closed
2 months ago
5
cellbender -> pytorch -> disk full, but it is not!
#58
smoe
closed
3 months ago
3
Add support for background matrix in `decontX`
#57
nictru
closed
3 months ago
0
Allow skip of ambient_removal by introducing method 'none'
#56
smoe
closed
3 months ago
5
Use raw cellranger outputs for cellbender
#55
nictru
closed
3 months ago
3
Add support for h5 input format
#54
nictru
closed
3 months ago
1
cellbender needs raw count matrix as input
#53
fbnrst
closed
3 months ago
0
48 add support for h5 input format
#52
fbnrst
closed
3 months ago
1
CELDA_DECONTX - bails out over negative size factors
#51
smoe
closed
2 months ago
13
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