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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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[Batch integration feature] HVG conservation easily hacked
#744
scottgigante-immunai
closed
1 year ago
1
[Dimensionality reduction] Fix RMSE metric
#743
scottgigante-immunai
closed
1 year ago
0
Issues with DR/metrics/RMSE
#742
scottgigante-immunai
closed
1 year ago
0
Update scib louvain and igraph
#741
scottgigante-immunai
closed
1 year ago
0
Revert "Update scib louvain and igraph"
#740
scottgigante-immunai
closed
1 year ago
0
Update scib louvain and igraph
#739
scottgigante-immunai
closed
1 year ago
0
Update sagemaker requirement from ==2.116.* to ==2.119.* in /docker/openproblems
#738
dependabot[bot]
closed
1 year ago
1
Bump jaxlib from 0.3.22 to 0.3.25 in /docker/openproblems-python-pytorch
#737
dependabot[bot]
closed
1 year ago
1
Update protobuf requirement from ==3.20.* to ==4.21.* in /docker/openproblems-python-tensorflow
#736
dependabot[bot]
closed
1 year ago
1
Build images in PR if same repo owner
#735
scottgigante-immunai
closed
1 year ago
0
Remove raw values for all-nan metrics
#734
scottgigante-immunai
closed
1 year ago
0
Split torch from non-torch dependencies
#733
scottgigante-immunai
closed
1 year ago
1
Revert "upgrade louvain and scib"
#732
scottgigante-immunai
closed
1 year ago
0
Update scvi-tools requirement from ~=0.16 to ~=0.19 in /docker/openproblems-r-pytorch
#731
dependabot[bot]
closed
1 year ago
3
Check for nf rate limiting
#730
scottgigante-immunai
closed
1 year ago
2
Publish both raw and scaled scores
#729
scottgigante-immunai
closed
1 year ago
0
Run builds in parallel
#728
scottgigante-immunai
closed
1 year ago
0
Upgrade DCA and tf2.4
#727
scottgigante-immunai
closed
1 year ago
0
separate bedtools from everything else
#726
scottgigante-immunai
closed
1 year ago
0
upgrade louvain and scib
#725
scottgigante-immunai
closed
1 year ago
1
set num_samples=2 in test mode
#724
scottgigante-immunai
closed
1 year ago
1
Use mnnpy from base repo
#723
scottgigante-immunai
closed
1 year ago
1
GitHub Actions are taking a really long time
#722
rcannood
closed
1 year ago
1
Update sagemaker requirement from ==2.116.* to ==2.118.* in /docker/openproblems
#721
dependabot[bot]
closed
1 year ago
2
Convert references to bib
#720
scottgigante-immunai
closed
1 year ago
5
Bump tensorflow from 2.9.0 to 2.9.3 in /docker/openproblems-python-tensorflow
#719
dependabot[bot]
closed
1 year ago
6
scanvi runs over an hour in test mode
#718
scottgigante-immunai
closed
1 year ago
4
cell2location runs over an hour in test mode
#717
scottgigante-immunai
closed
1 year ago
7
Website PR fix
#716
scottgigante-immunai
closed
1 year ago
0
Push task readmes to website from main
#715
scottgigante-immunai
closed
1 year ago
0
Turn off ci skip
#714
rcannood
closed
1 year ago
1
Send raw files to NBT repro
#713
scottgigante-immunai
closed
1 year ago
0
DR baseline: just use true features but smaller in test
#712
scottgigante-immunai
closed
1 year ago
3
Remove sagemaker compatibility from docker images
#711
scottgigante-immunai
opened
1 year ago
3
Make "Majority Vote" a baseline method
#710
rcannood
opened
1 year ago
9
make celltype clusters tighter in celltype random embedding/graph
#709
scottgigante-immunai
closed
1 year ago
6
Upload coverage in a single job
#707
scottgigante-immunai
closed
1 year ago
0
Add cell cycle score baseline
#706
scottgigante-immunai
closed
1 year ago
14
Add spectral baseline to dimensionality reduction
#705
scottgigante-immunai
closed
1 year ago
1
cell2location with max normalisation flexibility
#704
vitkl
closed
1 year ago
10
Store mean scaled metric as "mean score"
#703
scottgigante-immunai
closed
1 year ago
1
Fix proportions test
#702
scottgigante-immunai
closed
1 year ago
2
Put sample cells and genes in the repo
#701
scottgigante-immunai
closed
1 year ago
3
Change Cell2location to compute proportions
#700
vitkl
closed
1 year ago
9
add ncells to seuratv3 test mode
#699
scottgigante-immunai
closed
1 year ago
1
Fix references to `adata.layers["counts"]`
#698
scottgigante-immunai
closed
1 year ago
2
Run test benchmark in Tower
#697
scottgigante-immunai
closed
1 year ago
0
Use scanpy hvg with batch key instead of scib package
#696
adamgayoso
opened
1 year ago
1
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
opened
1 year ago
4
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