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openpipelines-bio
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openpipeline
https://openpipelines.bio
MIT License
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Feature/labels transfer
#221
VladimirShitov
closed
8 months ago
10
Fix hvg subsetting bug
#385
VladimirShitov
closed
10 months ago
8
Add LSI
#552
SarahOuologuem
opened
7 months ago
7
Implement reference mapping components
#138
VladimirShitov
closed
1 year ago
7
Add genetic demultiplexing component
#165
wxicu
closed
1 year ago
6
Fix cellranger_mkfastq and cellranger_count intergration tests hanging on CI.
#52
DriesSchaumont
closed
1 year ago
6
Refactor the TotalVI component to also allow running without reference
#546
ddemaeyer
opened
7 months ago
5
Demultiplication workflow
#51
tverbeiren
closed
1 year ago
5
Add missing -with-trace to nextflow integration tests.
#50
DriesSchaumont
closed
1 year ago
5
Feature/bbknn workflow
#456
mauro-saporita
closed
9 months ago
4
ATAC components
#398
SarahOuologuem
opened
11 months ago
4
Add TOTALVI integration method
#386
VladimirShitov
closed
9 months ago
4
first commit liana tool
#344
mauro-saporita
closed
1 year ago
4
Add genetic demultiplexing component
#343
rcannood
closed
6 months ago
4
Feature/popv
#135
MatthiasBeyens
closed
1 year ago
4
add script to download scgpt test resources
#750
dorien-er
closed
1 month ago
3
Capitalized modality names are not processed by full pipeline workflow
#626
KaiWaldrant
opened
4 months ago
3
refactor cellxgene census component
#621
rcannood
closed
1 week ago
3
Docker image for correction_cellbender_remove_background process refers to, but does not define PS1
#611
robsyme
closed
3 months ago
3
cluster/leiden config contains incorrect Markdown references
#590
JasperVandenberghen
closed
6 months ago
3
GEX/FB intersection module
#519
Isabelle-b
closed
5 months ago
3
refactor nxf state management in harmony leiden
#513
rcannood
closed
8 months ago
3
Add essential functionalities to enable gdo modality analysis
#444
MatthiasBeyens
closed
8 months ago
3
Implement cellranger multi conversion component
#152
DriesSchaumont
closed
1 year ago
3
Large refactor
#79
rcannood
closed
1 year ago
3
Fix multimodal integration tests by adding 'obs_covariates' argument to pipeline.
#63
DriesSchaumont
closed
1 year ago
3
Uniformise key parameters
#56
rcannood
closed
1 year ago
3
Implement harmonypy component & make changes to concat
#54
DriesSchaumont
closed
1 year ago
3
Update containers
#30
DriesSchaumont
closed
1 year ago
3
Pipeline examples
#3
ddemaeyer
closed
1 year ago
3
Port single sample pipeline
#1
ddemaeyer
closed
1 year ago
3
scGPT embedding component
#761
dorien-er
closed
4 days ago
2
Generate scgpt cross check genes module
#758
jakubmajercik
closed
4 days ago
2
Add extra test utilities, logging and asserters
#697
DriesSchaumont
closed
2 months ago
2
Don't rebuild containers for viash-hub.
#648
DriesSchaumont
closed
3 months ago
2
Remove big binary files
#622
rcannood
opened
5 months ago
2
Use the viash dependencies config value for workflows
#606
DriesSchaumont
closed
3 months ago
2
Viash 0.8.x
#599
rcannood
closed
5 months ago
2
Add dsb component
#588
wxicu
opened
6 months ago
2
Rework mitochondrial gene detection
#585
DriesSchaumont
closed
6 months ago
2
Use correct parameter name for model output in scvi_leiden
#562
DriesSchaumont
closed
7 months ago
2
Wrong memory assignment
#556
ddemaeyer
closed
6 months ago
2
Add calculate_qc_metrics component to ingestion pipelines
#541
ddemaeyer
closed
6 months ago
2
Add percent mitochondrial genes to the output of the filter_with_counts filter
#540
ddemaeyer
closed
6 months ago
2
Feature/cellxgene census update
#520
MatthiasBeyens
closed
7 months ago
2
full_pipeline - TypeError: boolean value of NA is ambiguous
#488
sarahbonnin
closed
9 months ago
2
The number of genes in a cell has to be pushed to the obs layer
#454
ddemaeyer
closed
10 months ago
2
nextflow tower add pipeline setup
#450
rhodesch
closed
9 months ago
2
Added modality passing to harmony pipeline
#449
ddemaeyer
closed
10 months ago
2
Add generic launch.json for debugging unittests and running python files.
#438
DriesSchaumont
closed
10 months ago
2
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