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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
41
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12
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Update scanpy GPU image
#130
nictru
closed
1 week ago
1
Add LIANA
#129
nictru
closed
2 weeks ago
1
Update gpu implementation
#128
nictru
closed
2 weeks ago
1
Add option for gene name unification
#127
nictru
closed
2 weeks ago
1
Add support for setting QC thresholds to zero
#126
nictru
opened
2 weeks ago
1
Use hackathon modules
#125
nictru
closed
2 weeks ago
1
Plot fixing
#124
paulinefx
closed
3 weeks ago
1
Legends cropped in multiQC results
#123
paulinefx
closed
3 weeks ago
0
Adding a description and changing the results order
#122
paulinefx
closed
3 weeks ago
2
SOLO returns doublet instead of singlets
#121
LeonHafner
closed
3 weeks ago
0
Fix error in usage
#120
LeonHafner
closed
4 weeks ago
1
Implement gene regulatory network analyses
#119
nictru
opened
1 month ago
0
Create nf-core module for SCDS
#118
nictru
opened
1 month ago
0
Create nf-core module for DoubletDetection
#117
nictru
closed
3 weeks ago
0
Create nf-core module for Scrublet
#116
nictru
opened
1 month ago
0
Create nf-core module for SOLO
#115
nictru
closed
3 weeks ago
0
Create nf-core module for scAR
#114
nictru
closed
3 weeks ago
2
Create nf-core module for DecontX
#113
nictru
opened
1 month ago
0
Create nf-core module for SoupX
#112
nictru
opened
1 month ago
0
Create nf-core subworkflow for Cellbender empty droplet detection
#111
nictru
closed
6 days ago
1
Create nf-core module for Cellbender background removal
#110
nictru
closed
3 weeks ago
0
Move preprocessing modules to nf-core/modules
#109
nictru
opened
1 month ago
0
Improve `preprocess_only` implementation
#108
nictru
opened
1 month ago
4
Implement cell-cell interaction analyses
#107
nictru
opened
1 month ago
0
Allow doublet detection score calculation without actually removing doublets
#106
nictru
opened
1 month ago
0
scanpy GPU containers fail
#105
KallyopeComp
closed
1 week ago
5
MultiQC config not found
#104
marcus-tutert
closed
1 month ago
0
Important! Template update for nf-core/tools v3.0.2
#103
nf-core-bot
closed
1 month ago
2
Important! Template update for nf-core/tools v3.0.1
#102
nf-core-bot
closed
1 month ago
1
Important! Template update for nf-core/tools v3.0.0
#101
nf-core-bot
closed
1 month ago
1
Add preprocess_only parameter
#100
nictru
closed
1 month ago
1
Add label specific UMAP and clustering option
#99
nictru
closed
2 months ago
1
Add support to Celltypist for non-human species.
#98
tbrittoborges
closed
2 months ago
0
Add MT percentage filtering
#97
tbrittoborges
closed
2 months ago
4
Allow using reference model without base adata
#96
nictru
closed
2 months ago
1
Add support for learning an scANVI model based on a given scVI model and cell type annotations
#95
nictru
closed
2 months ago
0
Fix problems with `counts` layer references
#94
nictru
closed
2 months ago
1
Add support for rank_genes_groups
#93
nictru
closed
2 months ago
1
Add PAGA calculation and improve reporting
#92
nictru
closed
2 months ago
1
Counts layer required for Scds and Solo is missing
#91
pakiessling
closed
2 months ago
0
Pipeline not running correctly on GPU
#90
pakiessling
closed
2 months ago
5
Fix `meta.expected_cells` not passing to commnad call (#88)
#89
tbrittoborges
closed
2 months ago
1
Add option for per-sample specification of doublet detection thresholds
#88
nictru
opened
2 months ago
0
Add MT percentage filtering
#87
nictru
closed
2 months ago
0
Fix cellbender dependency problem
#86
nictru
closed
2 months ago
1
Add support for cellbender expected cells
#85
nictru
closed
2 months ago
1
Implement meta.expected_cells (cellbender)
#84
tbrittoborges
closed
2 months ago
1
MultiQC fails with latest dev release
#83
alexblaessle
opened
2 months ago
0
Add rapids implementations for more tools
#82
nictru
closed
2 months ago
1
Add sample size table
#81
nictru
closed
2 months ago
1
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