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YosefLab
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mrvi-reproducibility
Nextflow pipeline for MrVI pipelines
BSD 3-Clause "New" or "Revised" License
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Notebook for comparing learned sample embeddings to local distance matrices
#67
justjhong
opened
1 month ago
0
Admissibility analysis on held out data
#66
justjhong
opened
1 month ago
0
Crohn's analysis notebook
#65
justjhong
closed
4 months ago
0
Rename scviv2 to mrvi
#64
justjhong
closed
7 months ago
0
updated ablation
#63
PierreBoyeau
closed
8 months ago
0
[WIP]: Simulation adjustment
#62
PierreBoyeau
opened
1 year ago
1
[WIP] add counterfactual reconstruction plot to haniffa notebook
#61
justjhong
closed
1 year ago
0
Sciplex updates
#60
justjhong
closed
6 months ago
0
GSEA with offline option
#59
justjhong
closed
1 year ago
0
[WIP] hca work for nir
#58
justjhong
closed
1 year ago
0
more complex simulations
#57
PierreBoyeau
closed
1 year ago
0
Clean up semisyn notebook
#56
justjhong
closed
1 year ago
0
More flexible runs + updated hparams
#55
PierreBoyeau
closed
1 year ago
0
add subsampling exp and associated notebook
#54
justjhong
closed
1 year ago
0
updated baselines
#53
PierreBoyeau
closed
1 year ago
0
Remove all traces of old mrvi
#52
justjhong
closed
1 year ago
0
Small u options
#51
justjhong
closed
1 year ago
0
Fix
#50
PierreBoyeau
closed
1 year ago
0
fix reqs
#49
PierreBoyeau
closed
1 year ago
0
fix path error
#48
PierreBoyeau
closed
1 year ago
0
New simple DEG filter
#47
justjhong
closed
1 year ago
0
Subsampling Experiment
#46
justjhong
closed
1 year ago
0
Add composition baseline variant functionality
#45
justjhong
closed
1 year ago
0
New datasets
#44
PierreBoyeau
closed
1 year ago
0
Sciplex autocorrelation notebook
#43
justjhong
closed
1 year ago
0
Move tree utils out into own file
#42
justjhong
closed
1 year ago
0
Cleanup pipeline, add documentation
#41
martinkim0
closed
1 year ago
1
Move sciplex analysis notebook into pipeline, and add sciplex specific metrics
#40
justjhong
closed
1 year ago
0
remove tsne
#39
PierreBoyeau
closed
1 year ago
0
Expand results
#38
PierreBoyeau
closed
1 year ago
0
Generic script to analyze results
#37
PierreBoyeau
closed
1 year ago
0
Sciplex analysis
#36
justjhong
closed
1 year ago
0
Load xarray in utils
#35
justjhong
opened
1 year ago
0
Integrate new normalized distances
#34
justjhong
closed
1 year ago
0
Experimental notebook for alternative distances/similarities
#33
justjhong
closed
1 year ago
1
Add option to run on AWS batch
#32
martinkim0
opened
1 year ago
0
Use `scib_metrics.Benchmarker` for metrics
#31
martinkim0
opened
1 year ago
0
Migrate relevant code bits to `scvi-v2`
#30
PierreBoyeau
opened
1 year ago
0
Uncertainty, cell-specific distance matrices, supervised analyses
#29
PierreBoyeau
opened
1 year ago
0
Add option to run MrVI only
#28
PierreBoyeau
closed
1 year ago
1
Include new data sets
#27
PierreBoyeau
opened
1 year ago
3
Plotting utils
#26
PierreBoyeau
opened
1 year ago
0
DEG module subworkflow
#25
PierreBoyeau
opened
1 year ago
0
UMAP/TSNE representations subworkflow
#24
PierreBoyeau
closed
1 year ago
0
Save all generated files' path
#23
PierreBoyeau
closed
1 year ago
1
remote-pdb option
#22
PierreBoyeau
closed
1 year ago
0
[WIP] Output distances for compositional approaches
#21
PierreBoyeau
closed
1 year ago
1
Merge script vs baselines
#20
PierreBoyeau
closed
1 year ago
0
scib-metrics limitations with data comprising only one batch
#19
PierreBoyeau
closed
1 year ago
0
Failing to install `scvi-tools` within the nextflow pipeline
#18
PierreBoyeau
closed
1 year ago
1
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