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openproblems-bio
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openproblems
Formalizing and benchmarking open problems in single-cell genomics
MIT License
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77
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Use scanpy hvg with batch key instead of scib package
#696
adamgayoso
closed
2 days ago
2
Counts being passed to scvi-tools models?
#695
adamgayoso
closed
1 year ago
10
Use scib-metrics implementations for batch integration embedding task
#694
adamgayoso
closed
2 days ago
5
Matrixed CI
#693
scottgigante-immunai
closed
1 year ago
1
Batch integration result metrics are not in proper range
#692
adamgayoso
closed
1 year ago
9
Bump nf-openproblems to v1.9
#691
scottgigante-immunai
closed
1 year ago
1
Update sagemaker requirement from ==2.116.* to ==2.117.* in /docker/openproblems
#690
dependabot[bot]
closed
1 year ago
2
add plotting functions from scib
#689
danielStrobl
closed
2 days ago
5
Metric odds ratio fix
#688
dbdimitrov
closed
1 year ago
2
Update keras requirement from <2.11,>=2.4 to >=2.4,<2.12 in /docker/openproblems-python-tf2.4
#687
dependabot[bot]
closed
1 year ago
2
add perfect celltype mixing baseline
#686
scottgigante-immunai
closed
1 year ago
1
batch integration baselines are suboptimal
#685
scottgigante-immunai
closed
1 year ago
6
All `odds_ratio` calls return 0
#684
scottgigante-immunai
closed
1 year ago
2
Combat (scaled) returns NaN in PC Regression
#683
scottgigante-immunai
closed
1 year ago
8
kBET returns NaN
#682
scottgigante-immunai
closed
1 year ago
2
Handle NaNs in nextflow export
#681
scottgigante-immunai
closed
1 year ago
2
Pancreas counts are not integers
#680
rcannood
closed
1 year ago
2
Add scripts for datasets
#679
rcannood
closed
2 days ago
8
Run pip check on build
#678
scottgigante-immunai
closed
1 year ago
1
Update bslib to 0.4.1
#677
github-actions[bot]
closed
1 year ago
1
Update styler to 1.8.1
#676
github-actions[bot]
closed
1 year ago
1
Run pip check to enforce no dependency conflicts
#675
scottgigante-immunai
closed
1 year ago
4
test dataset API on full datasets
#674
scottgigante-immunai
closed
2 days ago
6
break up _metrics into separate functions
#673
scottgigante-immunai
closed
1 year ago
2
Update IRkernel to 1.3.1
#672
github-actions[bot]
closed
1 year ago
1
Update bioc/batchelor to 1.14.0
#671
github-actions[bot]
closed
1 year ago
0
Update bioc/scran to 1.26.0
#670
github-actions[bot]
closed
1 year ago
0
Update boto3 requirement from ==1.25.* to ==1.26.* in /docker/openproblems
#669
dependabot[bot]
closed
1 year ago
2
retry failed request
#668
scottgigante-immunai
closed
1 year ago
2
Revert "Revert "bump louvain to 0.8""
#667
scottgigante-immunai
closed
1 year ago
1
Revert "bump louvain to 0.8"
#666
scottgigante-immunai
closed
1 year ago
0
Additional labels tests
#665
scottgigante-immunai
closed
1 year ago
1
Update pkgload to 1.3.1
#664
github-actions[bot]
closed
1 year ago
1
Update scvi-tools requirement from ~=0.17 to ~=0.19 in /docker/openproblems-python-scvi
#663
dependabot[bot]
closed
1 year ago
27
Update scvi-tools requirement from ==0.16.* to ==0.19.* in /docker/openproblems-python-extras
#662
dependabot[bot]
closed
1 year ago
1
Update torch requirement from ==1.12.* to ==1.13.* in /docker/openproblems-r-pytorch
#661
dependabot[bot]
closed
1 year ago
1
Update tabulate requirement from <0.9 to <0.10
#660
dependabot[bot]
closed
2 days ago
4
Update RcppAnnoy to 0.0.20
#659
github-actions[bot]
closed
1 year ago
1
Update sagemaker requirement from ==2.113.* to ==2.116.* in /docker/openproblems
#658
dependabot[bot]
closed
1 year ago
1
Update ragg to 1.2.4
#657
github-actions[bot]
closed
1 year ago
1
Update sagemaker requirement from ==2.113.* to ==2.115.* in /docker/openproblems
#656
dependabot[bot]
closed
1 year ago
2
Update sagemaker requirement from ==2.113.* to ==2.114.* in /docker/openproblems
#655
dependabot[bot]
closed
1 year ago
2
Update rpy2 requirement from <3.5.5 to <3.5.6
#654
dependabot[bot]
closed
1 year ago
1
Update e1071 to 1.7-12
#653
github-actions[bot]
closed
1 year ago
1
Update styler to 1.8.0
#652
github-actions[bot]
closed
1 year ago
1
Update boto3 requirement from ==1.24.* to ==1.25.* in /docker/openproblems
#651
dependabot[bot]
closed
1 year ago
1
Update snakemake requirement from <7.15,>=7.8 to >=7.8,<7.17
#650
dependabot[bot]
closed
1 year ago
1
use just one batch of pancreas data
#649
scottgigante-immunai
closed
1 year ago
3
make merge_keys available in adata.uns
#648
scottgigante-immunai
closed
1 year ago
1
add short metric descriptions to README
#647
danielStrobl
closed
1 year ago
5
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