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Mye-InfoBank
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scRAFIKI
A nextflow pipeline for processing sc-RNASeq data, performing QC and integration and preparing the results for further investigation using cellxgene.
BSD 3-Clause "New" or "Revised" License
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scHPL
#58
nictru
closed
6 months ago
0
Implement CI/CD workflow
#57
nictru
closed
6 months ago
0
Implement multiple pipeline modes
#56
nictru
closed
6 months ago
0
Implement a second iteration to the pipeline
#55
nictru
closed
7 months ago
0
Support RNAse R effect correction
#54
nictru
closed
7 months ago
0
Support pseudo aligners
#53
nictru
closed
7 months ago
0
Fix problems with small batches during doublet detection
#52
nictru
closed
8 months ago
0
Implement detection for problems in input files
#51
nictru
closed
8 months ago
0
Implement support for adding custom metadata columns and including certain genes to HVGs
#50
nictru
closed
8 months ago
0
Fix problems with tmp mount in apptainer (Diana's Leistung)
#49
nictru
closed
8 months ago
0
Fix bug with SOLO if batch size is smaller than 128
#48
nictru
closed
8 months ago
0
Make HVG identification more robust when low expression values are present
#47
nictru
closed
8 months ago
0
Switch to constant threshold for minimum cells to keep genes
#46
nictru
closed
8 months ago
0
Fix problems with dots in gene symbols
#45
nictru
closed
8 months ago
0
Make celltypes optional
#44
nictru
closed
8 months ago
0
Implement correlation analysis for clusterings
#43
nictru
closed
8 months ago
0
Implement a second iteration to the pipeline
#42
nictru
closed
7 months ago
0
Add option for regressing out cycling, mitochondrial and ribosomal influences
#41
nictru
opened
8 months ago
3
Switch to hard threshold of minimum cells to keep a gene
#40
nictru
closed
8 months ago
3
Implement cellbender as ambient RNA correction method
#39
nictru
opened
8 months ago
0
Fix problems with dots in gene symbols
#38
nictru
closed
8 months ago
0
4 implement scarches
#37
nictru
closed
8 months ago
0
32 make sure important marker genes are available
#36
nictru
closed
8 months ago
0
Implement cell type distribution plots
#35
nictru
closed
8 months ago
0
Implement per-cell QC metrics
#34
nictru
closed
8 months ago
0
Add QC metrics to cellxgene
#33
nictru
closed
8 months ago
1
Make sure important marker genes are available
#32
nictru
closed
8 months ago
2
Improve doublet removal
#31
nictru
closed
9 months ago
0
Add cell type composition plots for metadata fields
#30
nictru
closed
8 months ago
0
Implement sc-SHC
#29
nictru
closed
9 months ago
0
Implement composition analysis
#28
nictru
closed
9 months ago
0
Add dataset metadata composition analysis
#27
nictru
closed
9 months ago
0
Add more normalization methods
#26
nictru
closed
9 months ago
0
Add an additional way of investigating differential expression between clusters
#25
nictru
opened
9 months ago
4
Implement clustering QC analysis
#24
nictru
closed
9 months ago
4
Add guide for using cellXgene with our output format from a celltype-expert perspective
#23
nictru
closed
9 months ago
1
Investigate potential usage of GPU acceleration
#22
nictru
closed
8 months ago
0
Add cell-cycle annotation
#21
nictru
closed
10 months ago
0
Implement benchmarking
#20
nictru
closed
10 months ago
0
Simplify pipeline structure
#19
nictru
closed
10 months ago
0
Implement R-based integration methods using scib-pipeline
#18
nictru
opened
10 months ago
1
Investigate additional doublet detection methods
#17
nictru
closed
8 months ago
0
normalisation row issue fixed
#16
serareif
closed
10 months ago
0
Investigate resource usage of cellxgene on Oscar
#15
nictru
closed
9 months ago
3
Investigate additional annotation methods
#14
nictru
closed
8 months ago
0
Implement removal of ambient RNA using decontX
#13
nictru
closed
1 year ago
0
Add option for processing Seurat objects
#12
nictru
closed
9 months ago
3
Implement additional python-based integration methods
#11
nictru
closed
10 months ago
3
Improve clustering
#10
nictru
closed
1 year ago
0
Implement scIB
#9
nictru
closed
10 months ago
2
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