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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
5
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2
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Use raw cellranger outputs for cellbender
#55
nictru
opened
1 day ago
2
Add support for h5 input format
#54
nictru
closed
1 day ago
1
cellbender needs raw count matrix as input
#53
fbnrst
opened
1 day ago
0
48 add support for h5 input format
#52
fbnrst
closed
1 day ago
1
CELDA_DECONTX - bails out over negative size factors
#51
smoe
opened
1 day ago
7
Fix singularity cache problems
#50
nictru
closed
1 day ago
1
MPLCONFIGDIR expected in $HOME outside what singularity allows
#49
smoe
closed
1 day ago
2
Add support for h5 input format
#48
nictru
closed
1 day ago
1
Update docs
#47
nictru
closed
2 days ago
1
Add citations
#46
nictru
closed
2 weeks ago
1
Implement custom filtering
#45
nictru
closed
2 weeks ago
1
Implement singleR celltype annotation
#44
nictru
opened
2 weeks ago
2
Update documentation of supported ambient RNA removal methods
#43
nictru
closed
2 weeks ago
1
Implement celltypist cell type assignment
#42
nictru
closed
2 weeks ago
1
Implement scar ambient rna removal
#41
nictru
closed
2 weeks ago
1
Implement soupx ambient rna removal
#40
nictru
closed
2 weeks ago
1
Implement cellbender ambient rna removal
#39
nictru
closed
2 weeks ago
1
Implement scds doublet detection
#38
nictru
closed
2 weeks ago
1
Implement doubletdetection doublet detection
#37
nictru
closed
2 weeks ago
1
Implement scrublet doublet detection
#36
nictru
closed
2 weeks ago
1
Implement seurat integration
#35
nictru
closed
2 weeks ago
1
Implement combat integration
#34
nictru
closed
2 weeks ago
1
Implement bbknn integration
#33
nictru
closed
2 weeks ago
1
Implement harmony integration
#32
nictru
closed
2 weeks ago
1
Implement scAR ambient RNA removal
#31
nictru
closed
2 weeks ago
2
Add support for CSV input
#30
nictru
closed
2 weeks ago
1
Add support for count matrices as pipeline input
#29
nictru
closed
2 weeks ago
0
Add test configurations
#28
nictru
closed
2 weeks ago
2
Implement cellbender ambient RNA removal
#27
nictru
closed
2 weeks ago
0
Implement soupX ambient RNA removal
#26
nictru
closed
2 weeks ago
0
Implement methods for ambient RNA removal
#25
nictru
closed
2 weeks ago
1
Implement SingleR cell type assignment
#24
nictru
opened
2 weeks ago
0
Implement scPred cell type assignment
#23
nictru
opened
2 weeks ago
0
Implement Azimuth cell type assignment
#22
nictru
opened
2 weeks ago
0
Implement celltypist cell type assignment
#21
nictru
closed
2 weeks ago
0
Implement cell type assignment methods
#20
nictru
opened
2 weeks ago
3
Implement SCDS doublet detection
#19
nictru
closed
2 weeks ago
0
Implement DoubletFinder doublet detection
#18
nictru
opened
2 weeks ago
0
Implement DoubletDecon doublet detection
#17
nictru
opened
2 weeks ago
0
Implement DoubletDetection doublet detection
#16
nictru
closed
2 weeks ago
0
Implement Scrublet doublet detection
#15
nictru
closed
2 weeks ago
1
Implement doublet detection methods
#14
nictru
opened
2 weeks ago
1
Implement integration benchmarking using scIB
#13
nictru
opened
2 weeks ago
0
Implement Seurat integration
#12
nictru
closed
2 weeks ago
0
Implement LIGER integration
#11
nictru
opened
2 weeks ago
0
Implement Harmony integration
#10
nictru
closed
2 weeks ago
0
Implement Combat integration
#9
nictru
closed
2 weeks ago
0
Implement BBKNN integration
#8
nictru
closed
2 weeks ago
0
Implement integration methods
#7
nictru
opened
2 weeks ago
2
Implement pathway analysis using decoupler
#6
nictru
opened
2 weeks ago
3
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