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[status] 2024-01-15 12:11:48 UTC
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actions-user committed Jan 15, 2024
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31 changes: 16 additions & 15 deletions README.md
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107 changes: 60 additions & 47 deletions index.html
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55 changes: 40 additions & 15 deletions repos.csv
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Original file line number Diff line number Diff line change
@@ -68,7 +68,7 @@ theislab,cellrank,theislab/cellrank,281,7,11,35,FALSE,https://github.com/theisla

* Update format test

* Remove scvelo git install",[![](https://github.com/theislab/cellrank/workflows/Test/badge.svg)](https://github.com/theislab/cellrank/actions/runs/7441629419) [![](https://github.com/theislab/cellrank/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank/actions/runs/7441681902)
* Remove scvelo git install",[![](https://github.com/theislab/cellrank/workflows/Test/badge.svg)](https://github.com/theislab/cellrank/actions/runs/7522637260) [![](https://github.com/theislab/cellrank/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank/actions/runs/7522691210)
theislab,cellrank2_reproducibility,theislab/cellrank2_reproducibility,3,1,0,0,FALSE,https://github.com/theislab/cellrank2_reproducibility,3,9ab01c87a34c5ecbc36293fdb07e209ec3b9f17e,"Update `notebooks/index.md` (#45)

Update Jupyter book index page s.t. it matches repository README to
@@ -82,7 +82,7 @@ theislab,consensus-clustering-evaluation,theislab/consensus-clustering-evaluatio
theislab,countae,theislab/countae,1,4,0,0,FALSE,https://github.com/theislab/countae,1,NA,NA,NA
theislab,covid-perturbation,theislab/covid-perturbation,3,3,0,0,FALSE,https://github.com/theislab/covid-perturbation,3,NA,NA,NA
theislab,covid_macrophages_integration,theislab/covid_macrophages_integration,2,5,0,4,FALSE,https://github.com/theislab/covid_macrophages_integration,2,NA,NA,NA
theislab,cpa,theislab/cpa,66,4,12,13,FALSE,https://github.com/theislab/cpa,66,NA,NA,NA
theislab,cpa,theislab/cpa,66,4,13,13,FALSE,https://github.com/theislab/cpa,66,NA,NA,NA
theislab,cpa-reproducibility,theislab/cpa-reproducibility,7,3,0,1,FALSE,https://github.com/theislab/cpa-reproducibility,7,NA,NA,NA
theislab,cross_system_integration,theislab/cross_system_integration,9,2,10,0,FALSE,https://github.com/theislab/cross_system_integration,9,NA,NA,NA
theislab,dali,theislab/dali,0,7,0,1,FALSE,https://github.com/theislab/dali,0,NA,NA,NA
@@ -93,24 +93,24 @@ theislab,diffxpy,theislab/diffxpy,169,6,106,22,FALSE,https://github.com/theislab
theislab,diffxpy_tutorials,theislab/diffxpy_tutorials,10,8,4,2,FALSE,https://github.com/theislab/diffxpy_tutorials,10,NA,NA,NA
theislab,disent,theislab/disent,5,3,0,0,FALSE,https://github.com/theislab/disent,5,NA,NA,NA
theislab,edgepy,theislab/edgepy,0,3,0,0,FALSE,https://github.com/theislab/edgepy,0,NA,NA,NA
theislab,ehrapy,theislab/ehrapy,90,7,32,9,FALSE,https://github.com/theislab/ehrapy,90,84d33c8988ea560aa557fbe6a99b926befa84457,"Add test windows
theislab,ehrapy,theislab/ehrapy,90,7,33,9,FALSE,https://github.com/theislab/ehrapy,90,84d33c8988ea560aa557fbe6a99b926befa84457,"Add test windows

Signed-off-by: zethson <lukas.heumos@posteo.net>",[![](https://github.com/theislab/ehrapy/workflows/Test%20windows%20stuff/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/5577003787)
theislab,ehrapy,theislab/ehrapy,90,7,32,9,FALSE,https://github.com/theislab/ehrapy,90,e7fe5b7362566f4a2fee8fd47cbd77cdf228aa13,"[pre-commit.ci] pre-commit autoupdate (#636)
theislab,ehrapy,theislab/ehrapy,90,7,33,9,FALSE,https://github.com/theislab/ehrapy,90,e7fe5b7362566f4a2fee8fd47cbd77cdf228aa13,"[pre-commit.ci] pre-commit autoupdate (#636)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.1.11)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",[![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7452254841) [![](https://github.com/theislab/ehrapy/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7452254844) [![](https://github.com/theislab/ehrapy/workflows/Test/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7452254836) [![](https://github.com/theislab/ehrapy/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7452254842) [![](https://github.com/theislab/ehrapy/workflows/Check%20Build/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7452254848)
theislab,ehrapy,theislab/ehrapy,90,7,32,9,FALSE,https://github.com/theislab/ehrapy,90,ea6b4430d58d4ff8660eb15bd5db4d248f1c74ea,"Submodule
theislab,ehrapy,theislab/ehrapy,90,7,33,9,FALSE,https://github.com/theislab/ehrapy,90,ea6b4430d58d4ff8660eb15bd5db4d248f1c74ea,"Submodule

Signed-off-by: zethson <lukas.heumos@posteo.net>",[![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7260760638)
theislab,ehrapy-cli,theislab/ehrapy-cli,1,3,0,0,FALSE,https://github.com/theislab/ehrapy-cli,1,NA,NA,NA
theislab,ehrapy-datasets,theislab/ehrapy-datasets,4,2,0,2,FALSE,https://github.com/theislab/ehrapy-datasets,4,cb7707afc4523a317cfb30c1d101091adfaa44cd,Add mimic-2 to CI,[![](https://github.com/theislab/ehrapy-datasets/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/ehrapy-datasets/actions/runs/4510904353)
theislab,ehrapy-reproducibility,theislab/ehrapy-reproducibility,0,2,0,0,FALSE,https://github.com/theislab/ehrapy-reproducibility,0,NA,NA,NA
theislab,ehrapy-site,theislab/ehrapy-site,1,2,0,0,FALSE,https://github.com/theislab/ehrapy-site,1,NA,NA,NA
theislab,ehrapy-tutorials,theislab/ehrapy-tutorials,5,3,1,2,FALSE,https://github.com/theislab/ehrapy-tutorials,5,NA,NA,NA
theislab,ehrdata,theislab/ehrdata,3,3,3,1,FALSE,https://github.com/theislab/ehrdata,3,f673449fa25e9bf7668f3a87d293c4289032f7b2,add a temp notebook,[![](https://github.com/theislab/ehrdata/workflows/Check%20Build/badge.svg)](https://github.com/theislab/ehrdata/actions/runs/7478299191) [![](https://github.com/theislab/ehrdata/workflows/Test/badge.svg)](https://github.com/theislab/ehrdata/actions/runs/7478299205)
theislab,ehrdata,theislab/ehrdata,3,3,3,1,FALSE,https://github.com/theislab/ehrdata,3,f673449fa25e9bf7668f3a87d293c4289032f7b2,add a temp notebook,[![](https://github.com/theislab/ehrdata/workflows/Check%20Build/badge.svg)](https://github.com/theislab/ehrdata/actions/runs/7478299191) [![](https://github.com/theislab/ehrdata/workflows/Test/badge.svg)](https://github.com/theislab/ehrdata/actions/runs/7524573877)
theislab,enrichment_analysis_celltype,theislab/enrichment_analysis_celltype,9,5,0,4,FALSE,https://github.com/theislab/enrichment_analysis_celltype,9,NA,NA,NA
theislab,epicardiods_analysis,theislab/epicardiods_analysis,2,2,1,0,FALSE,https://github.com/theislab/epicardiods_analysis,2,NA,NA,NA
theislab,expiMap_reproducibility,theislab/expiMap_reproducibility,8,5,3,4,FALSE,https://github.com/theislab/expiMap_reproducibility,8,NA,NA,NA
@@ -125,7 +125,7 @@ API Update, Transform and ToIterable classes.",[![](https://github.com/theislab/
theislab,geome,theislab/geome,13,3,4,4,FALSE,https://github.com/theislab/geome,13,5bf0cd07b2ea7fa224a37f69232542a9e686c5bf,"Merge pull request #31 from theislab/template-update

Automated template update from cookiecutter-scverse",[![](https://github.com/theislab/geome/workflows/Sync%20Template/badge.svg)](https://github.com/theislab/geome/actions/runs/4904831582)
theislab,gh-dashboard,theislab/gh-dashboard,1,2,0,0,FALSE,https://github.com/theislab/gh-dashboard,1,0f519ac990c56741ece5cb83ee4cf51343babd59,[status] 2024-01-13 12:11:29 UTC,[![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/7518997327)
theislab,gh-dashboard,theislab/gh-dashboard,1,2,0,0,FALSE,https://github.com/theislab/gh-dashboard,1,9537be22014a8526b4e8c3a662ecbc04ae8c2d49,[status] 2024-01-14 12:11:33 UTC,[![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/7528531503)
theislab,graph_abstraction,theislab/graph_abstraction,26,8,0,10,FALSE,https://github.com/theislab/graph_abstraction,26,NA,NA,NA
theislab,greatpy,theislab/greatpy,8,3,4,0,FALSE,https://github.com/theislab/greatpy,8,NA,NA,NA
theislab,gut_lineage,theislab/gut_lineage,2,3,0,3,FALSE,https://github.com/theislab/gut_lineage,2,NA,NA,NA
@@ -162,6 +162,31 @@ theislab,intercode,theislab/intercode,6,3,1,1,FALSE,https://github.com/theislab/
theislab,ipsc_ipd_analysis,theislab/ipsc_ipd_analysis,0,3,0,0,FALSE,https://github.com/theislab/ipsc_ipd_analysis,0,NA,NA,NA
theislab,kBET,theislab/kBET,138,9,8,23,FALSE,https://github.com/theislab/kBET,138,NA,NA,NA
theislab,kbranches,theislab/kbranches,5,7,0,0,FALSE,https://github.com/theislab/kbranches,5,NA,NA,NA
theislab,moscot,theislab/moscot,78,3,38,6,FALSE,https://github.com/theislab/moscot,78,924c78a124b48b3a791a2d188d1ba3aa112535ba,"Cost Tests (#637)

* added tests for cost utils

* add barcode distance tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix naming

* refactor for precommit

* added tests for leaf_distance

* fix docstring formatting

* fixed the tests

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Dominik Klein <dominik.klein@helmoltz-munich.de>
Co-authored-by: Dominik Klein <dominik.klein@helmholtz-munich.de>",[![](https://github.com/theislab/moscot/workflows/Lint/badge.svg)](https://github.com/theislab/moscot/actions/runs/7522644709) [![](https://github.com/theislab/moscot/workflows/Test/badge.svg)](https://github.com/theislab/moscot/actions/runs/7522601879)
theislab,moscot,theislab/moscot,78,3,38,6,FALSE,https://github.com/theislab/moscot,78,b233601b6aecd7259aaa1a5dba107f2963420614,"Update/lrgw2 (#613)


@@ -173,7 +198,7 @@ theislab,moscot_benchmarks,theislab/moscot_benchmarks,1,2,1,0,FALSE,https://gith
theislab,moscot_not,theislab/moscot_not,2,2,8,0,FALSE,https://github.com/theislab/moscot_not,2,NA,NA,NA
theislab,moscot_notebooks,theislab/moscot_notebooks,6,1,6,2,FALSE,https://github.com/theislab/moscot_notebooks,6,bbca9f2b0243c4349e0cdd98c78af083251cfe9c,"Merge pull request #58 from theislab/fix/func_calls

small fixes for warnings and function calls",[![](https://github.com/theislab/moscot_notebooks/workflows/lint/badge.svg)](https://github.com/theislab/moscot_notebooks/actions/runs/7441656473)
small fixes for warnings and function calls",[![](https://github.com/theislab/moscot_notebooks/workflows/lint/badge.svg)](https://github.com/theislab/moscot_notebooks/actions/runs/7522666307)
theislab,moslin,theislab/moslin,9,1,0,1,FALSE,https://github.com/theislab/moslin,9,NA,NA,NA
theislab,mouse_cross-condition_pancreatic_islet_atlas,theislab/mouse_cross-condition_pancreatic_islet_atlas,7,2,0,3,FALSE,https://github.com/theislab/mouse_cross-condition_pancreatic_islet_atlas,7,NA,NA,NA
theislab,mubind,theislab/mubind,19,3,30,0,FALSE,https://github.com/theislab/mubind,19,NA,NA,NA
@@ -194,13 +219,13 @@ theislab,organoid_dexamethason_stimulation,theislab/organoid_dexamethason_stimul
theislab,paga,theislab/paga,176,10,21,30,FALSE,https://github.com/theislab/paga,176,NA,NA,NA
theislab,pancreas-targeted_pharmacology,theislab/pancreas-targeted_pharmacology,0,7,0,2,FALSE,https://github.com/theislab/pancreas-targeted_pharmacology,0,NA,NA,NA
theislab,pancreatic-endocrinogenesis,theislab/pancreatic-endocrinogenesis,4,3,0,5,FALSE,https://github.com/theislab/pancreatic-endocrinogenesis,4,NA,NA,NA
theislab,pertpy,theislab/pertpy,68,4,30,15,FALSE,https://github.com/theislab/pertpy,68,404835c82f9a3d943b85973c10130303d090839d,"Revert ""Deleted JaxscgenPlot""
theislab,pertpy,theislab/pertpy,68,4,32,15,FALSE,https://github.com/theislab/pertpy,68,404835c82f9a3d943b85973c10130303d090839d,"Revert ""Deleted JaxscgenPlot""

This reverts commit 161fc137c5a23320a5799a22cd4d7212b550bca9.",[![](https://github.com/theislab/pertpy/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/pertpy/actions/runs/4629618853)
theislab,pertpy,theislab/pertpy,68,4,30,15,FALSE,https://github.com/theislab/pertpy,68,c95bbcb5d95f224b7a574c95b3c1c7fc1a51d2a3,"Refactor mixscape
theislab,pertpy,theislab/pertpy,68,4,32,15,FALSE,https://github.com/theislab/pertpy,68,d00c5f9e7243d6b1984becf973509f5f8ae425fc,pre-commit,[![](https://github.com/theislab/pertpy/workflows/Release/badge.svg)](https://github.com/theislab/pertpy/actions/runs/6737423407)
theislab,pertpy,theislab/pertpy,68,4,32,15,FALSE,https://github.com/theislab/pertpy,68,d49872c25180c652743a8153daea3026cffc13a6,"Fix adjusttext forces

Signed-off-by: zethson <lukas.heumos@posteo.net>",[![](https://github.com/theislab/pertpy/workflows/Labeler/badge.svg)](https://github.com/theislab/pertpy/actions/runs/7512245148)
theislab,pertpy,theislab/pertpy,68,4,30,15,FALSE,https://github.com/theislab/pertpy,68,d00c5f9e7243d6b1984becf973509f5f8ae425fc,pre-commit,[![](https://github.com/theislab/pertpy/workflows/Release/badge.svg)](https://github.com/theislab/pertpy/actions/runs/6737423407)
Signed-off-by: zethson <lukas.heumos@posteo.net>",[![](https://github.com/theislab/pertpy/workflows/Labeler/badge.svg)](https://github.com/theislab/pertpy/actions/runs/7520214398) [![](https://github.com/theislab/pertpy/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/pertpy/actions/runs/7520214404) [![](https://github.com/theislab/pertpy/workflows/Check%20Build/badge.svg)](https://github.com/theislab/pertpy/actions/runs/7520214399) [![](https://github.com/theislab/pertpy/workflows/Test/badge.svg)](https://github.com/theislab/pertpy/actions/runs/7520214400)
theislab,pertpy-datasets,theislab/pertpy-datasets,1,3,0,1,FALSE,https://github.com/theislab/pertpy-datasets,1,NA,NA,NA
theislab,pertpy-tutorials,theislab/pertpy-tutorials,4,4,2,6,FALSE,https://github.com/theislab/pertpy-tutorials,4,NA,NA,NA
theislab,perturbation-metrics,theislab/perturbation-metrics,4,2,1,0,FALSE,https://github.com/theislab/perturbation-metrics,4,NA,NA,NA
@@ -224,7 +249,7 @@ theislab,scanpy-in-R,theislab/scanpy-in-R,12,3,1,0,FALSE,https://github.com/thei
theislab,scanpy.org,theislab/scanpy.org,0,7,1,0,FALSE,https://github.com/theislab/scanpy.org,0,NA,NA,NA
theislab,scanpy_neighbors,theislab/scanpy_neighbors,0,3,0,1,FALSE,https://github.com/theislab/scanpy_neighbors,0,NA,NA,NA
theislab,scanpy_squidpy_demo_2021,theislab/scanpy_squidpy_demo_2021,2,4,0,0,FALSE,https://github.com/theislab/scanpy_squidpy_demo_2021,2,NA,NA,NA
theislab,scanpydoc,theislab/scanpydoc,12,6,4,5,FALSE,https://github.com/theislab/scanpydoc,12,fa7285660b1f046b51993642bc42802e06cfd154,"Override the search keyboard combination, too (#128)",[![](https://github.com/theislab/scanpydoc/workflows/Python%20tests/badge.svg)](https://github.com/theislab/scanpydoc/actions/runs/7503195912)
theislab,scanpydoc,theislab/scanpydoc,12,6,2,5,FALSE,https://github.com/theislab/scanpydoc,12,ef5491a72f66c437ff2ac5f33364e162e1813be2,Fix search interactions (#132),[![](https://github.com/theislab/scanpydoc/workflows/Python%20tests/badge.svg)](https://github.com/theislab/scanpydoc/actions/runs/7527423469)
theislab,scarches,theislab/scarches,294,14,34,48,FALSE,https://github.com/theislab/scarches,294,NA,NA,NA
theislab,scarches_notebooks,theislab/scarches_notebooks,0,3,0,0,FALSE,https://github.com/theislab/scarches_notebooks,0,NA,NA,NA
theislab,scatac_poisson_reproducibility,theislab/scatac_poisson_reproducibility,6,3,0,0,FALSE,https://github.com/theislab/scatac_poisson_reproducibility,6,NA,NA,NA
@@ -243,7 +268,7 @@ theislab,scvelo,theislab/scvelo,371,13,55,100,FALSE,https://github.com/theislab/

Update version number.",[![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076514631) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076514630) [![](https://github.com/theislab/scvelo/workflows/Release/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076589652)
theislab,scvelo_notebooks,theislab/scvelo_notebooks,25,2,2,12,FALSE,https://github.com/theislab/scvelo_notebooks,25,NA,NA,NA
theislab,sfaira,theislab/sfaira,131,8,166,13,FALSE,https://github.com/theislab/sfaira,131,55bcbbf2588a08e4a98b1e65324119407ec6e75c,Merge pull request #741 from theislab/release,[![](https://github.com/theislab/sfaira/workflows/Check%20URLs/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7515648562)
theislab,sfaira,theislab/sfaira,131,8,166,13,FALSE,https://github.com/theislab/sfaira,131,55bcbbf2588a08e4a98b1e65324119407ec6e75c,Merge pull request #741 from theislab/release,[![](https://github.com/theislab/sfaira/workflows/Check%20URLs/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7522576396)
theislab,sfaira,theislab/sfaira,131,8,166,13,FALSE,https://github.com/theislab/sfaira,131,5fcf932c44613e6bf4063ef3075ad6062bf5d9a1,round restored counts in some affected datasets,[![](https://github.com/theislab/sfaira/workflows/Build%20sfaira%20Package/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672388) [![](https://github.com/theislab/sfaira/workflows/Create%20sfaira%20data-loader%20templates/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672382) [![](https://github.com/theislab/sfaira/workflows/Run%20bandit/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672385) [![](https://github.com/theislab/sfaira/workflows/Run%20flake8%20linting/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672384)
theislab,sfaira,theislab/sfaira,131,8,166,13,FALSE,https://github.com/theislab/sfaira,131,ceb14c946f699c38d18a32192b76d4639caf845e,fix download links,[![](https://github.com/theislab/sfaira/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/sfaira/actions/runs/6812817430)
theislab,sfaira-portal,theislab/sfaira-portal,0,4,2,0,FALSE,https://github.com/theislab/sfaira-portal,0,NA,NA,NA
@@ -388,7 +413,7 @@ updated-dependencies:
Signed-off-by: dependabot[bot] <support@github.com>",[![](https://github.com/theislab/spapros/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/spapros/actions/runs/6854088652) [![](https://github.com/theislab/spapros/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/spapros/actions/runs/6854088648)
theislab,spapros,theislab/spapros,20,3,15,5,FALSE,https://github.com/theislab/spapros,20,c4c0903758ecb1acd0e16c1d227e59e8be1e28de,"Merge pull request #288 from theislab/development

Mention python package in docs",[![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/5980912686) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/7516121105)
Mention python package in docs",[![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/5980912686) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/7523141362)
theislab,spapros-pipeline,theislab/spapros-pipeline,7,2,0,0,FALSE,https://github.com/theislab/spapros-pipeline,7,NA,NA,NA
theislab,spapros-smk,theislab/spapros-smk,0,2,0,1,FALSE,https://github.com/theislab/spapros-smk,0,NA,NA,NA
theislab,spapros_reproducibility,theislab/spapros_reproducibility,0,1,1,0,FALSE,https://github.com/theislab/spapros_reproducibility,0,NA,NA,NA

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