nf-core/scdownstream
A single cell transcriptomics pipeline for QC, integration and making the data presentable
NextflowMIT
Issues
- 1
additional output for cellbender
#75 opened by fbnrst - 4
Implement GPU support for relevant tools
#69 opened by nictru - 1
celltypist fails with value error
#72 opened by fbnrst - 13
CELDA_DECONTX - bails out over negative size factors
#51 opened by smoe - 0
AMBIENT_RNA_REMOVAL needs revision - runtime error ch_raw undefined with cellbender
#65 opened by smoe - 1
Minimal sample sheet with both filtered and unfiltered produced by scrnaseq triggers celda decontx runtime error
#64 opened by smoe - 1
Improve reporting
#2 opened by nictru - 0
Add support for background matrix in `decontX`
#57 opened by nictru - 3
cellbender -> pytorch -> disk full, but it is not!
#58 opened by smoe - 0
cellbender needs raw count matrix as input
#53 opened by fbnrst - 1
Add support for h5 input format
#48 opened by nictru - 2
- 3
Implement cell type assignment methods
#20 opened by nictru - 1
Implement methods for ambient RNA removal
#25 opened by nictru - 0
Implement celltypist cell type assignment
#21 opened by nictru - 2
Implement scAR ambient RNA removal
#31 opened by nictru - 0
Implement soupX ambient RNA removal
#26 opened by nictru - 0
Implement cellbender ambient RNA removal
#27 opened by nictru - 0
Implement SCDS doublet detection
#19 opened by nictru - 0
Implement DoubletDetection doublet detection
#16 opened by nictru - 0
Implement DoubletDecon doublet detection
#17 opened by nictru - 0
Implement DoubletFinder doublet detection
#18 opened by nictru - 1
Implement Scrublet doublet detection
#15 opened by nictru - 0
Implement Seurat integration
#12 opened by nictru - 0
Implement Combat integration
#9 opened by nictru - 0
Implement BBKNN integration
#8 opened by nictru - 0
Implement Harmony integration
#10 opened by nictru - 0
Add support for count matrices as pipeline input
#29 opened by nictru - 0
Add test datasets
#1 opened by nictru - 1
Implement doublet detection methods
#14 opened by nictru - 3
Implement pathway analysis using decoupler
#6 opened by nictru - 0
Implement pathway analysis
#3 opened by nictru - 2
Implement integration methods
#7 opened by nictru - 0
Implement SingleR cell type assignment
#24 opened by nictru - 0
Implement scPred cell type assignment
#23 opened by nictru - 0
Implement Azimuth cell type assignment
#22 opened by nictru - 0
Implement integration benchmarking using scIB
#13 opened by nictru - 0
Implement LIGER integration
#11 opened by nictru - 2
Implement pathway analysis using EnrichR
#4 opened by nictru - 0
Implement pathway analysis using WebGestaltR
#5 opened by nictru