template-repos.yml

- url: https://github.com/Bendemeurichy/FlowSOM_parallel
- url: https://github.com/BioImageTools/ngff-transformations
- url: https://github.com/Boehringer-Ingelheim/dso
- url: https://github.com/Boehringer-Ingelheim/dso-mgr
- url: https://github.com/BoevaLab/infercnvpy
- url: https://github.com/COMBINE-lab/QCatch
- url: https://github.com/CSOgroup/cellcharter
- url: https://github.com/CSOgroup/torchgmm
- url: https://github.com/ChanghaoGong/STutils
- url: https://github.com/ChengmingZhang-CAS/BrainBeacon
- url: https://github.com/ChengmingZhang-CAS/CauTrigger
- url: https://github.com/CompCy-lab/scHub
- url: https://github.com/Computational-Morphogenomics-Group/Ladder
- url: https://github.com/ComputationalBiomedicineGroup/Rectangle
- url: https://github.com/Floto-Lab/BactGraph
- url: https://github.com/FroeseLab/bulkpy
- url: https://github.com/Gabriellvl/FlowSOM
- url: https://github.com/Genentech/MoCAVI
- url: https://github.com/LiHongCSBLab/scMagnify
- url: https://github.com/Lotfollahi-lab/mintflow
- url: https://github.com/MannLabs/alphapepttools
- url: https://github.com/MannLabs/dvp-io
- url: https://github.com/Marcufong/CellFlow-UOT
- url: https://github.com/NKI-CCB/sobolev_alignment
- url: https://github.com/PMBio/scDoRI
- url: https://github.com/Teichlab/multi-view-atlas
- url: https://github.com/YosefLab/cytovi-reference-implementation
- url: https://github.com/YosefLab/embedding-scvi
- url: https://github.com/YosefLab/popV
- url: https://github.com/YosefLab/pycea
- url: https://github.com/YosefLab/scib-metrics
- url: https://github.com/YosefLab/scvi-hub-models
- url: https://github.com/YosefLab/treedata
- url: https://github.com/YosefLab/visionpy
- url: https://github.com/Zethson/fknni
- url: https://github.com/adamgayoso/figmasvg
- url: https://github.com/adamgayoso/umapjax
- url: https://github.com/aertslab/CREsted
- url: https://github.com/aertslab/TF-MINDI
- url: https://github.com/agerardy/myeditdistance
- url: https://github.com/angelolab/Nimbus-Inference
- url: https://github.com/angelolab/mbt
- url: https://github.com/angelolab/pici-vitessce
- url: https://github.com/angelolab/tonic-vitessce
- url: https://github.com/bartuschimschek/mmil-refactored
- url: https://github.com/bioFAM/mofaflex
- url: https://github.com/bioFAM/scDoRI
- url: https://github.com/bunina-lab/scDoRI_tools
- url: https://github.com/cameronraysmith/perturbvelo
- url: https://github.com/carmonalab/pyucell
- url: https://github.com/cellannotation/pairOT
- url: https://github.com/clinicalomx/napari-prism
- url: https://github.com/cobioda/scispy
- url: https://github.com/const-ae/pyLemur
- url: https://github.com/czi-ai/scldm
- url: https://github.com/d-j-k/donorpy
- url: https://github.com/data-intuitive/dummy-anndata
- url: https://github.com/davidrm-bio/DOTools_py
- url: https://github.com/decomverse/scmetric
- url: https://github.com/dertrotl/geneGATer
- url: https://github.com/devsystemslab/HNOCA-tools
- url: https://github.com/edbiomedai/scmorph
- url: https://github.com/emdann/pert2state_model
- url: https://github.com/ergonyc/lblator
- url: https://github.com/eroell/mypackage-cruft-oct
- url: https://github.com/greenelab/single_translator_VAE
- url: https://github.com/grst/karttapullautin2tiles
- url: https://github.com/grst/spatialdata-plot
- url: https://github.com/icbi-lab/atlas_protocol
- url: https://github.com/icbi-lab/infercnvpy
- url: https://github.com/icbi-lab/shears
- url: https://github.com/ilia-kats/PolarbearPlus
- url: https://github.com/immunitastx/monkeybread
- url: https://github.com/imsb-uke/nichepca
- url: https://github.com/ivirshup/binsparse-python
- url: https://github.com/jkobject/hierarchical_classifier
- url: https://github.com/jkobject/simpler_flash
- url: https://github.com/jlause/scverse-tutorials
- url: https://github.com/joechanlab/scDeBussy
- url: https://github.com/joschif/delnx
- url: https://github.com/jskerman/chronai
- url: https://github.com/karadavis-lab/nbl
- url: https://github.com/lhqing/scmallet
- url: https://github.com/lucas-diedrich/bpca
- url: https://github.com/lucas-diedrich/mulink
- url: https://github.com/lucas-diedrich/sccoral
- url: https://github.com/lueckenlab/patpy
- url: https://github.com/lzj1769/LR2net
- url: https://github.com/macwiatrak/BacBench
- url: https://github.com/macwiatrak/Bacformer
- url: https://github.com/macwiatrak/scverse-hackathon-data-4-ai
- url: https://github.com/mengerj/adata_hf_datasets
- url: https://github.com/mengerj/mmcontext
- url: https://github.com/mostafavilabuw/drum
- url: https://github.com/mumichae/scAtlasTb-utils
- url: https://github.com/nitzanlab/biolord
- url: https://github.com/peng-lab/hescape
- url: https://github.com/pinellolab/PerTurbo
- url: https://github.com/pinellolab/cell2net
- url: https://github.com/quadbio/atac_mapper
- url: https://github.com/quadbio/cell-annotator
- url: https://github.com/quadbio/cellmapper
- url: https://github.com/quadbio/scBulkDE
- url: https://github.com/quadbio/scembed
- url: https://github.com/quadbio/slurm_sweep
- url: https://github.com/rushin682/spatialstream
- url: https://github.com/saeyslab/FlowSOM_Python
- url: https://github.com/saezlab/MINA
- url: https://github.com/scverse/annbatch
- url: https://github.com/scverse/anndata
- url: https://github.com/scverse/anndata-plot
- url: https://github.com/scverse/cookiecutter-scverse-instance
  skip: true
  reason: Instance repo gets updated by the bot via the template
- url: https://github.com/scverse/decoupler
- url: https://github.com/scverse/deres
- url: https://github.com/scverse/formulaic-contrasts
- url: https://github.com/scverse/genomic-features
- url: https://github.com/scverse/mudata
- url: https://github.com/scverse/pertpy
- url: https://github.com/scverse/pytometry
- url: https://github.com/scverse/scanpy
- url: https://github.com/scverse/scirpy
- url: https://github.com/scverse/scverse-misc
- url: https://github.com/scverse/scverse-tutorials
- url: https://github.com/scverse/simple-scvi
- url: https://github.com/scverse/spatial-sample-aggregation
- url: https://github.com/scverse/spatialdata-plot
- url: https://github.com/scverse/squidpy
- url: https://github.com/srivarra/annsel
- url: https://github.com/srivarra/spatial-collection
- url: https://github.com/srivarra/xrdantic
- url: https://github.com/sueoglu/myeditdistance
- url: https://github.com/tansey-lab/nf-rnaseq
- url: https://github.com/tddough98/airgradient
- url: https://github.com/theislab/CellFlow
- url: https://github.com/theislab/CellFlow2
- url: https://github.com/theislab/DRVI
- url: https://github.com/theislab/cellflow_reproducibility
- url: https://github.com/theislab/cellink
- url: https://github.com/theislab/ehrapy
- url: https://github.com/theislab/ehrdata
- url: https://github.com/theislab/geome
- url: https://github.com/theislab/mapqc
- url: https://github.com/theislab/multigrate
- url: https://github.com/theislab/multimil
- url: https://github.com/theislab/spatialdata-db
- url: https://github.com/theislab/transcription_factor_activity
- url: https://github.com/theislab/troutpy
- url: https://github.com/timtreis/gefslim
- url: https://github.com/vitkl/cell2module
- url: https://github.com/vitkl/regularizedvi
- url: https://github.com/wangd12rpi/hescape_changed
- url: https://github.com/yizhak-lab-ccg/scXpand
- url: https://github.com/zunderlab/eschr