Skip to content

HISTORY.md

Latest commit

 

History

History
1206 lines (1092 loc) · 46.4 KB

HISTORY.md

File metadata and controls

1206 lines (1092 loc) · 46.4 KB

Changelog

(unreleased)

  • Updates doc tables. [Christophe Bécavin]

  • Release: version 0.7.0 🚀 [Christophe Bécavin]

  • Release: version 🚀 [Christophe Bécavin]

  • Release: version 🚀 [Christophe Bécavin]

  • Update doc. [Christophe Bécavin]

  • Merge pull request #50 from becavin-lab/metrics. [Christophe Becavin]

    Metrics

  • Update README.md. [Christophe Becavin]

  • Update README.md. [Christophe Becavin]

  • Fix typo in cell annotation metrics documentation. [Christophe Becavin]

  • Update metric type description in cell_annotation.md. [Christophe Becavin]

  • Release: version 0.6.2 🚀 [Christophe Bécavin]

  • Release: version 0.6.1 🚀 [Christophe Bécavin]

  • Merge branch 'main' of github.com:becavin-lab/checkatlas. [Christophe Bécavin]

  • Update README.md. [Christophe Becavin]

  • Add link to readthedocs. [Moccia]

  • Release: version 0.6.1 🚀 [Christophe Bécavin]

  • Release: version 0.6.0 🚀 [Christophe Bécavin]

  • Update docs. [Christophe Bécavin]

  • Format and linting. [Christophe Bécavin]

  • Add tutoria data1. [Moccia]

  • Merge pull request #49 from becavin-lab/metrics. [Christophe Becavin]

    Metrics

  • Add excel results. [Moccia]

  • Add entourage code. [Moccia]

  • Update co_knn.md. [LucaMariaMoccia]

  • Update clustering.md. [LucaMariaMoccia]

  • Create calinski_harabasz.md. [LucaMariaMoccia]

  • Modif tuto.sh. [Christophe Bécavin]

  • Add clustering & annotation & denoising metrics. [Moccia]

  • Update cell_annotation.md. [LucaMariaMoccia]

  • Update cell_annotation.md. [LucaMariaMoccia]

  • Update cell_annotation.md. [LucaMariaMoccia]

  • Create adj_mutual_info.md. [LucaMariaMoccia]

  • Fix relative imports. [Christophe Bécavin]

  • Update specificity.md. [LucaMariaMoccia]

  • Update dim_red.md. [LucaMariaMoccia]

  • Add running time. [Christophe Bécavin]

  • Remove for now cellranger. [Christophe Bécavin]

  • Update dim_red.md. [LucaMariaMoccia]

  • Rename docs/metrics/poisson.md to docs/metrics/denoising/poisson.md. [LucaMariaMoccia]

  • Rename docs/metrics/mse.md to docs/metrics/denoising/mse.md. [LucaMariaMoccia]

  • Create denoising.md. [LucaMariaMoccia]

  • Update specificity.md. [LucaMariaMoccia]

  • Update clustering.md. [LucaMariaMoccia]

  • Update dim_red.md. [LucaMariaMoccia]

  • Update cell_annotation.md. [LucaMariaMoccia]

  • Rename docs/metrics/luca/poisson.md to docs/metrics/poisson.md. [LucaMariaMoccia]

  • Rename docs/metrics/luca/mse.md to docs/metrics/mse.md. [LucaMariaMoccia]

  • Delete docs/metrics/luca/test.md. [LucaMariaMoccia]

  • Delete docs/metrics/luca/summary_table.md. [LucaMariaMoccia]

  • Delete docs/metrics/luca/sumary_test.md. [LucaMariaMoccia]

  • Rename docs/metrics/luca/all_metrics.md to docs/metrics/all_metrics.md. [LucaMariaMoccia]

  • Update dim_red.md. [LucaMariaMoccia]

  • Update clustering.md. [LucaMariaMoccia]

  • Update cell_annotation.md. [LucaMariaMoccia]

  • Rename pcr.md to pcr.md. [LucaMariaMoccia]

  • Rename nmi.md to nmi.md. [LucaMariaMoccia]

  • Rename kbet.md to kbet.md. [LucaMariaMoccia]

  • Rename f1_score.md to f1_score.md. [LucaMariaMoccia]

  • Rename hvg.md to hvg.md. [LucaMariaMoccia]

  • Rename graph_connectivity.md to graph_connectivity.md. [LucaMariaMoccia]

  • Rename cc_conservation.md to cc_conservation.md. [LucaMariaMoccia]

  • Rename lisi.md to lisi.md. [LucaMariaMoccia]

  • Rename asw.md to asw.md. [LucaMariaMoccia]

  • Rename adjusted_rand_index.md to adjusted_rand_index.md. [LucaMariaMoccia]

  • Rename fowlkes_mallows.md to fowlkes_mallows.md. [LucaMariaMoccia]

  • Rename mutual_information.md to mutual_information.md. [LucaMariaMoccia]

  • Rename rand.md to rand.md. [LucaMariaMoccia]

  • Rename v_measure.md to v_measure.md. [LucaMariaMoccia]

  • Rename kolmogorov_smirnov.md to kolmogorov_smirnov.md. [LucaMariaMoccia]

  • Rename dunn.md to dunn.md. [LucaMariaMoccia]

  • Rename dbcv.md to dbcv.md. [LucaMariaMoccia]

  • Rename dbi.md to dbi.md. [LucaMariaMoccia]

  • Rename silhouette.md to silhouette.md. [LucaMariaMoccia]

  • Rename kruskal_stress.md to kruskal_stress.md. [LucaMariaMoccia]

  • Rename spearman_rho.md to spearman_rho.md. [LucaMariaMoccia]

  • Rename distance_correlation.md to distance_correlation.md. [LucaMariaMoccia]

  • Rename density_preservation.md to density_preservation.md. [LucaMariaMoccia]

  • Rename ged.md to ged.md. [LucaMariaMoccia]

  • Rename ajd.md to ajd.md. [LucaMariaMoccia]

  • Rename entourage.md to entourage.md. [LucaMariaMoccia]

  • Rename co_knn.md to co_knn.md. [LucaMariaMoccia]

  • Rename trust_continuity.md to trust_continuity.md. [LucaMariaMoccia]

  • Rename lcmc.md to lcmc.md. [LucaMariaMoccia]

  • Rename global_local_coknn.md to global_local_coknn.md. [LucaMariaMoccia]

  • Create kendall_copy.md. [LucaMariaMoccia]

  • Delete docs/metrics/specificity/test.md. [LucaMariaMoccia]

  • Rename gini.md to gini.md. [LucaMariaMoccia]

  • Rename shannon.md to shannon.md. [LucaMariaMoccia]

  • Rename ova_ovm.md to ova_ovm.md. [LucaMariaMoccia]

  • Rename silhouette.md to silhouette_0.md. [LucaMariaMoccia]

  • Rename rand_index.md to rand_index_0.md. [LucaMariaMoccia]

  • Rename kruskal_stress.md to kruskal_stress_0.md. [LucaMariaMoccia]

  • Update dim_red.md. [LucaMariaMoccia]

  • Update specificity.md. [LucaMariaMoccia]

  • Update cell_annotation.md. [LucaMariaMoccia]

  • Update cell_annotation.md. [LucaMariaMoccia]

  • Update clustering.md. [LucaMariaMoccia]

  • Move nextflow back into checkatlas. [Christophe Bécavin]

  • Add nextflow to checkatlas from nf-core-checkatlas. [Christophe Bécavin]

  • Merge branch 'metrics' of github.com:becavin-lab/checkatlas into metrics. [Christophe Bécavin]

  • Create test.md. [LucaMariaMoccia]

  • Update cell_annotation.md. [Christophe Becavin]

  • Update clustering.md. [Christophe Becavin]

  • Update dim_red.md. [Christophe Becavin]

  • Update specificity.md. [Christophe Becavin]

  • Update spatial.md. [Christophe Becavin]

  • Add tables. [Becavin]

  • Update spatial.md. [Christophe Becavin]

  • Update spatial.md. [Christophe Becavin]

  • Update spatial.md. [Christophe Becavin]

  • Add tables. [Becavin]

  • Merge branch 'metrics' of github.com:becavin-lab/checkatlas into metrics. [Becavin]

  • Delete docs/metrics/luca/Feuille 1.html. [LucaMariaMoccia]

  • Update spatial. [Becavin]

  • Update entourage.md. [LucaMariaMoccia]

  • Update kolmogorov_smirnov.md. [LucaMariaMoccia]

  • Update entourage.md. [LucaMariaMoccia]

  • Add spatial section. [Becavin]

  • Update entourage.md. [LucaMariaMoccia]

  • Update ajd.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update ged.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update global_local_coknn.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update co_knn.md. [LucaMariaMoccia]

  • Update density_preservation.md. [LucaMariaMoccia]

  • Update distance_correlation.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update lcmc.md. [LucaMariaMoccia]

  • Update spearman_rho.md. [LucaMariaMoccia]

  • Update kruskal_stress.md. [LucaMariaMoccia]

  • Update trust_continuity.md. [LucaMariaMoccia]

  • Update r2.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update poisson.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update mse.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update pcr.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update nmi.md. [LucaMariaMoccia]

  • Update kbet.md. [LucaMariaMoccia]

  • Update f1_score.md. [LucaMariaMoccia]

  • Update f1_score.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update hvg.md. [LucaMariaMoccia]

  • Update graph_connectivity.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update graph_connectivity.md. [LucaMariaMoccia]

  • Update cc_conservation.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Delete docs/images/metrics/Cell_Cycle.png. [LucaMariaMoccia]

  • Update cc_conservation.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update lisi.md. [LucaMariaMoccia]

  • Update asw.md. [LucaMariaMoccia]

  • Update adjusted_rand_index.md. [LucaMariaMoccia]

  • Update rand.md. [LucaMariaMoccia]

  • Update tau.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update gini.md. [LucaMariaMoccia]

  • Update shannon.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update ova_ovm.md. [LucaMariaMoccia]

  • Update trust_continuity.md. [LucaMariaMoccia]

  • Update lcmc.md. [LucaMariaMoccia]

  • Update spearman_rho.md. [LucaMariaMoccia]

  • Update spearman_rho.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Delete docs/images/metrics/spearman.png. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update spearman_rho.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update kruskal_stress.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update kolmogorov_smirnov.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update v_measure.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update mutual_information.md. [LucaMariaMoccia]

  • Move nextflow back into checkatlas. [Christophe Bécavin]

  • Add files via upload. [LucaMariaMoccia]

  • Rename folwkes_mallows.png to fowlkes_mallows.png. [LucaMariaMoccia]

  • Update fowlkes_mallows.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update rand.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update dbcv.md. [LucaMariaMoccia]

  • Update dbcv.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update silhouette.md. [LucaMariaMoccia]

  • Update dbi.md. [LucaMariaMoccia]

  • Update entourage.md. [LucaMariaMoccia]

  • Update entourage.md. [LucaMariaMoccia]

  • Update dunn.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update dbi.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update dbi.md. [LucaMariaMoccia]

  • Update silhouette.md. [LucaMariaMoccia]

  • Update silhouette.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update entourage.md. [Christophe Becavin]

  • Update entourage.md. [Christophe Becavin]

  • Add files via upload. [Christophe Becavin]

  • Update sumary_test.md. [Christophe Becavin]

  • Update sumary_test.md. [Christophe Becavin]

  • Update sumary_test.md. [LucaMariaMoccia]

  • Create test.md. [LucaMariaMoccia]

  • Update and rename sumary_test.html to sumary_test.md. [LucaMariaMoccia]

  • Update and rename sumary_test.md to sumary_test.html. [LucaMariaMoccia]

  • Create sumary_test.md. [LucaMariaMoccia]

  • Create summary_table.md. [LucaMariaMoccia]

  • Add files via upload. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create kolmogorov_smirnov.md. [LucaMariaMoccia]

  • Release: version 0.5.6 🚀 [Becavin]

  • Modif relase workflow. [Becavin]

  • Release: version 0.5.5 🚀 [Becavin]

  • Modif relase workflow. [Becavin]

  • Release: version 0.5.4 🚀 [Becavin]

  • Continuous integration 🔄 tests-0.5.3. [Becavin]

  • Continuous integration 🔄 tests-0.5.3. [Becavin]

  • Continuous integration 🔄 tests-0.5.3. [Becavin]

  • Add macos and windows R installed in tests. [Becavin]

  • Continuous integration 🔄 tests-0.5.3. [Becavin]

  • Continuous integration 🔄 tests-0.5.3. [Becavin]

  • Add R in github actions. [Becavin]

  • Continuous integration 🔄 tests-0.5.3. [Becavin]

  • Continuous integration 🔄 tests-0.5.3. [Becavin]

  • Continuous integration 🔄 tests-0.5.3. [Becavin]

  • Continuous integration 🔄 tests-0.5.3. [Becavin]

  • Continuous integration 🔄 tests-0.5.2. [Becavin]

  • Continuous integration 🔄 tests-0.5.1. [Becavin]

  • Continuous integration 🔄 tests-0.5.0. [Becavin]

  • Continuous integration 🔄 tests-0.5.0. [Becavin]

  • Merge branch 'metrics' of github.com:becavin-lab/checkatlas into metrics. [Becavin]

  • Update ajd.md. [LucaMariaMoccia]

  • Update entourage.md. [LucaMariaMoccia]

  • Update ged.md. [LucaMariaMoccia]

  • Update global_local_coknn.md. [LucaMariaMoccia]

  • Update co_knn.md. [LucaMariaMoccia]

  • Update density_preservation.md. [LucaMariaMoccia]

  • Update distance_correlation.md. [LucaMariaMoccia]

  • Update r2.md. [LucaMariaMoccia]

  • Update r2.md. [LucaMariaMoccia]

  • Update poisson.md. [LucaMariaMoccia]

  • Update mse.md. [LucaMariaMoccia]

  • Update pcr.md. [LucaMariaMoccia]

  • Update nmi.md. [LucaMariaMoccia]

  • Update kbet.md. [LucaMariaMoccia]

  • Update f1_score.md. [LucaMariaMoccia]

  • Update hvg.md. [LucaMariaMoccia]

  • Update graph_connectivity.md. [LucaMariaMoccia]

  • Update cc_conservation.md. [LucaMariaMoccia]

  • Update lisi.md. [LucaMariaMoccia]

  • Update asw.md. [LucaMariaMoccia]

  • Update adjusted_rand_index.md. [LucaMariaMoccia]

  • Update gini.md. [LucaMariaMoccia]

  • Update shannon.md. [LucaMariaMoccia]

  • Update ova_ovm.md. [LucaMariaMoccia]

  • Update trust_continuity.md. [LucaMariaMoccia]

  • Update lcmc.md. [LucaMariaMoccia]

  • Update spearman_rho.md. [LucaMariaMoccia]

  • Update kruskal_stress.md. [LucaMariaMoccia]

  • Update v_measure.md. [LucaMariaMoccia]

  • Update fowlkes_mallows.md. [LucaMariaMoccia]

  • Update rand.md. [LucaMariaMoccia]

  • Update dunn.md. [LucaMariaMoccia]

  • Update dbi.md. [LucaMariaMoccia]

  • Update silhouette.md. [LucaMariaMoccia]

  • Add dev dependencies. [Becavin]

  • Update packages dependecies, switching to python 3.12, and removing unecessary dep. [Becavin]

  • Update adjusted_rand_index.md. [Christophe Becavin]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create ged.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Update ajd.md. [LucaMariaMoccia]

  • Update ajd.md. [LucaMariaMoccia]

  • Update silhouette.md. [LucaMariaMoccia]

  • Update mkdocs. [Becavin]

  • Create ajd.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create entourage.md. [LucaMariaMoccia]

  • Update silhouette.md. [LucaMariaMoccia]

  • Update tau.md. [LucaMariaMoccia]

  • Update gini.md. [LucaMariaMoccia]

  • Update shannon.md. [LucaMariaMoccia]

  • Update ova_ovm.md. [LucaMariaMoccia]

  • Update trust_continuity.md. [LucaMariaMoccia]

  • Update lcmc.md. [LucaMariaMoccia]

  • Update spearman_rho.md. [LucaMariaMoccia]

  • Update kruskal_stress.md. [LucaMariaMoccia]

  • Update v_measure.md. [LucaMariaMoccia]

  • Update mutual_information.md. [LucaMariaMoccia]

  • Update fowlkes_mallows.md. [LucaMariaMoccia]

  • Update rand.md. [LucaMariaMoccia]

  • Update dbcv.md. [LucaMariaMoccia]

  • Update dbi.md. [LucaMariaMoccia]

  • Update dunn.md. [LucaMariaMoccia]

  • Update dbi.md. [LucaMariaMoccia]

  • Update silhouette.md. [LucaMariaMoccia]

  • Create test.png. [Christophe Becavin]

  • Merge branch 'metrics' of github.com:becavin-lab/checkatlas into metrics. [Becavin]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Modify file names. [Christophe Bécavin]

  • Update kruskal_stress.md. [LucaMariaMoccia]

  • Update silhouette.md. [LucaMariaMoccia]

  • Update lcmc.md. [LucaMariaMoccia]

  • Update trust_continuity.md. [LucaMariaMoccia]

  • Update spearman_rho.md. [LucaMariaMoccia]

  • Update kruskal_stress.md. [LucaMariaMoccia]

  • Update trust_continuity.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create global_local_coknn.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create distance_correlation.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create desnity_preservation.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create co_knn.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create r2.md. [LucaMariaMoccia]

  • Create poisson.md. [LucaMariaMoccia]

  • Create mse.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create pcr.md. [LucaMariaMoccia]

  • Update nmi.md. [LucaMariaMoccia]

  • Create nmi.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Update kbet.md. [LucaMariaMoccia]

  • Create kbet.md. [LucaMariaMoccia]

  • Update f1_score.md. [LucaMariaMoccia]

  • Create f1_score.md. [LucaMariaMoccia]

  • Update hvg.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Update asw.md. [LucaMariaMoccia]

  • Create hvg.md. [LucaMariaMoccia]

  • Update graph_connectivity.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create graph_connectivity.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create cc_conservation.md. [LucaMariaMoccia]

  • Create lisi.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create asw.md. [LucaMariaMoccia]

  • Update adjusted_rand_index.md. [LucaMariaMoccia]

  • Update adjusted_rand_index.md. [LucaMariaMoccia]

  • Create adjusted_rand_index.md. [LucaMariaMoccia]

  • Remove Rapport_AC_metrics folder. [Christophe Bécavin]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Update and rename notready_ova_ovo.md to ova_ovm.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create tau.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create gini.md. [LucaMariaMoccia]

  • Rename ova_ovo.md to notready_ova_ovo.md. [LucaMariaMoccia]

  • Update ova_ovo.md. [LucaMariaMoccia]

  • Create shannon.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create ova_ovo.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create trust_continuity.md. [LucaMariaMoccia]

  • Update lcmc.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

    lcmc

  • Create lcmc.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

    spearman

  • Create spearman_rho.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

    kruskal

  • Create kruskal_stress.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create v_measure.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create mutual_information.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

    fowlkes mallows

  • Create fowlkes_mallows.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

    add rand

  • Create rand.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

    dbcv

  • Create dbcv.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

    add dunn

  • Create dunn.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

    dbi

  • Create dbi.md. [LucaMariaMoccia]

  • Update all_metrics.md. [LucaMariaMoccia]

  • Create silhouette.md. [LucaMariaMoccia]

    silhouette translated + code source

  • Create all_metrics.md. [LucaMariaMoccia]

  • Modif folder/files names. [Christophe Bécavin]

  • Merge branch 'metrics' of github.com:becavin-lab/checkatlas into metrics. [Christophe Bécavin]

  • Create LCMC.md. [LucaMariaMoccia]

  • Fix file name doc. [Christophe Bécavin]

  • Merge branch 'metrics' of github.com:becavin-lab/checkatlas into metrics sss. [Christophe Bécavin]

  • Update All_DimRed.md. [LucaMariaMoccia]

  • Create Spearman_rho.md. [LucaMariaMoccia]

  • Update All_DimRed.md. [LucaMariaMoccia]

  • Update All_Clustering_metrics.md. [LucaMariaMoccia]

  • Create All_DimRed.md. [LucaMariaMoccia]

  • Update Kruskal.md. [LucaMariaMoccia]

    Il faut écrire en LaTeX la formule, ça bugge

  • Rename All_metrics.md to All_Clustering_metrics.md. [LucaMariaMoccia]

  • Rename docs/metrics/Rapport_AC_metrics/All_metrics.md to docs/metrics/Rapport_AC_metrics/Clustering/All_metrics.md. [LucaMariaMoccia]

  • Update All_metrics.md. [LucaMariaMoccia]

  • Update All_metrics.md. [LucaMariaMoccia]

  • Rename Kruskal to Kruskal.md. [LucaMariaMoccia]

  • Update All_metrics.md. [LucaMariaMoccia]

  • Update All_metrics.md. [LucaMariaMoccia]

  • Update and rename V_Measure to V_Measure.md. [LucaMariaMoccia]

    V-measure

  • Update V_Measure. [LucaMariaMoccia]

  • Create V_Measure. [LucaMariaMoccia]

  • Update Mutual_Information.md. [LucaMariaMoccia]

    Mutual Information

  • Create Mutual_Information.md. [LucaMariaMoccia]

  • Update DBCV.md. [LucaMariaMoccia]

  • Update Davies_Bouldin.md. [LucaMariaMoccia]

  • Update Dunn.md. [LucaMariaMoccia]

  • Update Fowlkes_Mallows.md. [LucaMariaMoccia]

  • Update Rand_Index.md. [LucaMariaMoccia]

  • Update Silhouette.md. [LucaMariaMoccia]

  • Update Fowlkes_Mallows.md. [LucaMariaMoccia]

  • Delete docs/metrics/Luca/h. [LucaMariaMoccia]

  • Create h. [LucaMariaMoccia]

  • Create Fowlkes_Mallows.md. [LucaMariaMoccia]

  • Update and rename Index.md to All_metrics.md. [LucaMariaMoccia]

    Metrics Antoine liens

  • Rename Davies-Bouldin.md to Davies_Bouldin.md. [LucaMariaMoccia]

  • Create DBCV.md. [LucaMariaMoccia]

    DBCV à verifier

  • Create Dunn.md. [LucaMariaMoccia]

    Dunn Index

  • Update Silhouette.md. [LucaMariaMoccia]

    Sillhoeutte V2

  • Create Rand_Index.md. [LucaMariaMoccia]

    rand index

  • Update Silhouette.md. [LucaMariaMoccia]

    Silhouette avce LaTeX + sources

  • Create Silhouette.md. [LucaMariaMoccia]

    Cmd+C Cmd+V de Silhouette à partr de main

  • Update and rename CLUSTERING.Index.md to Index.md. [LucaMariaMoccia]

    exemple de comment écrire un recap avec lien qui renvoie au doc

  • Create CLUSTERING.Index.md. [LucaMariaMoccia]

  • Update Davies-Bouldin.md. [LucaMariaMoccia]

  • Update Davies-Bouldin.md. [LucaMariaMoccia]

    almost done

  • Update and rename Davies-Bouldin to Davies-Bouldin.md. [LucaMariaMoccia]

  • Update Davies-Bouldin. [LucaMariaMoccia]

    test

  • Create Davies-Bouldin. [LucaMariaMoccia]

    metrics n°2 for section clustering (the first one beeing Silhouette, already created)

  • Create Kruskal. [LucaMariaMoccia]

    add dir for metrics in report A. Collin

  • Delete docs/metrics/fhgfhgfhg directory. [LucaMariaMoccia]

  • Create Rapport_AC. [LucaMariaMoccia]

    add dir for metrics in Antoine Collin report

  • Modify mkdocs. [Christophe Bécavin]

  • Add clustering table. [christophe Becavin]

  • Release: version 0.4.17 🚀 [Christophe Bécavin]

  • Fix Docs make. [Christophe Bécavin]

  • Format, Lint, and fix tests. [Christophe Bécavin]

  • Release: version 0.4.16 🚀 [Christophe Bécavin]

  • Release: version 0.4.15 🚀 [Christophe Bécavin]

  • Fix docs make files. [Christophe Bécavin]

  • Release: version 0.4.14 🚀 [Christophe Bécavin]

  • Release: version 0.4.13 🚀 [Christophe Bécavin]

  • Release: version 0.4.12 🚀 [Christophe Bécavin]

  • Release: version 0.4.11 🚀 [Christophe Bécavin]

  • Release: version 0.4.10 🚀 [Christophe Bécavin]

  • Release: version 0.4.9 🚀 [Christophe Bécavin]

  • Release: version 0.4.8 🚀 [Christophe Bécavin]

  • Release: version 0.4.7 🚀 [Christophe Bécavin]

  • Release: version 0.4.6 🚀 [Christophe Bécavin]

  • Release: version 0.4.5 🚀 [Christophe Bécavin]

  • Release: version 0.4.4 🚀 [Christophe Bécavin]

  • Release: version 0.4.3 🚀 [Christophe Bécavin]

  • Add examples with celltypist data. [Christophe Bécavin]

  • Clean metrics docs and py files. Prepare for adding all metrics. [Christophe Bécavin]

  • Premier push metrics branch. [Christophe Bécavin]

  • Update silhouette.md. [Christophe Becavin]

    add sections

  • Update silhouette.md. [Christophe Becavin]

    add silhouette modif

  • Update README.md. [Christophe Becavin]

  • Update README. [Christophe Bécavin]

  • Update README. [Christophe Bécavin]

  • Update README. [Christophe Bécavin]

  • Update readme and doc. [Christophe Bécavin]

  • Update readme and doc. [Christophe Bécavin]

  • Release: version 0.4.2 🚀 [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.4.2. [Christophe Bécavin]

  • Update readme and doc. [Christophe Bécavin]

  • Release: version 0.4.1 🚀 [drbecavin]

  • Continuous integration 🔄 tests-0.4.1. [drbecavin]

  • Update README.md. [Christophe Becavin]

  • Update README and docs. [drbecavin]

  • Update README.md. [Christophe Becavin]

  • Update README. [drbecavin]

  • ISMB ECCB release. [Christophe Bécavin]

  • Release: version 0.4.0 🚀 [Christophe Bécavin]

  • ISMB ECCB release. [Christophe Bécavin]

  • Fix examples display. [Christophe Bécavin]

  • Fix readme. [drbecavin]

  • Add example in ReaDME. [drbecavin]

  • Release: version 0.3.12 🚀 [drbecavin]

  • Continuous integration 🔄 tests-0.3.12. [drbecavin]

  • Modify readmle and docs. [drbecavin]

  • Release: version 0.3.11 🚀 [drbecavin]

  • Release: version 0.3.11 🚀 [drbecavin]

  • Modify readmle and docs. [drbecavin]

  • Release: version 0.3.10 🚀 [drbecavin]

  • Continuous integration 🔄 tests-0.3.10. [drbecavin]

  • Add exampleto docs. [drbecavin]

  • Merge branch 'main' of github.com:becavin-lab/checkatlas yeswq. [Christophe Bécavin]

  • Clean examples. [drbecavin]

  • Add example 5. [Christophe Bécavin]

  • Update examples notebok. [Christophe Bécavin]

  • Update examples, put them in docs, put jupyter ntbook examples in docs. [Christophe Bécavin]

  • Update examples. [Christophe Bécavin]

  • Release: version 0.3.9 🚀 [Christophe Bécavin]

  • Ready for new release with improved html reports. [Christophe Bécavin]

  • Fix html reports creation. [Christophe Bécavin]

  • Release: version 0.3.8 🚀 [Christophe Bécavin]

  • Remove qc, uma,tsne from multiqc custom content. [Christophe Bécavin]

  • Release: version 0.3.7 🚀 [Christophe Bécavin]

  • Newreleasewith cellranger management improved. [Christophe Bécavin]

  • Add multiple cellranger types management. Clustering and reductions from subfolders in outs folder are processed for Cellranger v1to v7and Cellranger arc (multiome) [Christophe Bécavin]

  • Release: version 0.3.6 🚀 [Christophe Bécavin]

  • Release: version 0.3.6 🚀 [Christophe Bécavin]

  • Fix html reports production. [Christophe Bécavin]

  • Add version display. [Christophe Bécavin]

  • Release: version 0.3.5 🚀 [Christophe Bécavin]

  • Release: version 0.3.5 🚀 [Christophe Bécavin]

  • Release: version 0.3.5 🚀 [Christophe Bécavin]

  • Release: version 0.3.5 🚀 [Christophe Bécavin]

  • Release: version 0.3.5 🚀 [Christophe Bécavin]

  • Release: version 0.3.5 🚀 [Christophe Bécavin]

  • Some minor modif. [Christophe Bécavin]

  • Add list scanpy, list seurat, list cellranger. [Christophe Bécavin]

  • Release: version 0.3.4 🚀 [Christophe Bécavin]

  • Add checkatlas-workflow executable. [Christophe Bécavin]

  • Release: version 0.3.3 🚀 [Christophe Bécavin]

  • Add checkatlas-workflow executable for search and html reports. [Christophe Bécavin]

  • Release: version 0.3.2 🚀 [Christophe Bécavin]

  • Add test data. [Christophe Bécavin]

  • Release: version 0.3.1 🚀 [Christophe Bécavin]

  • Modify tables extension for multiqc to work. [Christophe Bécavin]

  • Fix dc. [Christophe Bécavin]

  • Release: version 0.3.0 🚀 [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.3.0. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.3.0. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.3.0. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.3.0. [Christophe Bécavin]

  • Update tests functions. [Christophe Bécavin]

  • Merge pull request #38 from becavin-lab/nf-core. [drbecavin]

    Nf core

  • Remove obsolete function, update init files. [Christophe Bécavin]

  • Ready to switch to woorkflow nf-core; Checkatlas reduced to iits simplest. [Christophe Bécavin]

  • Add Seurat processes in checkatlas executable. [Christophe Bécavin]

  • Modify seurat for future nextflow workflow. [Christophe Bécavin]

  • Modify all checkatlas architecture, ready to develop nf-core workflow. [Christophe Bécavin]

  • Add checkatlas process command line: summary, qc, metric_cluster, etc... [Christophe Bécavin]

  • Add saving to pandas csv the list of atlases found, and checkatlas.read_list_atlases function. [Christophe Bécavin]

  • Add Ceation of samplesheet table with all atlas information. [Christophe Bécavin]

  • Put back atlas_info, but as a dictionnary. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Remove seurat tests becauyse Seurat is impossible to install on github actions. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.16. [Christophe Bécavin]

  • Modif install Seurat for github workflow. [Christophe Bécavin]

  • Release: version 0.2.16 🚀 [Christophe Bécavin]

  • Release: version 0.2.15 🚀 [Christophe Bécavin]

  • New release after tests implementation. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Fix Seurat install. [Christophe Bécavin]

  • Fix Seurat install. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Move back test outside of checkatlas package. BUGFIX : .gitignore was wrongly configured and was ignoring datasets.py. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Add datasets for test. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Move tests in checkatlas package. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Release: version 0.2.15 🚀 [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Clean init.py in tests. [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.15. [Christophe Bécavin]

  • Modify atlas_seurat docstrings. [Christophe Bécavin]

  • Modify atlas_seurat docstrings. [Christophe Bécavin]

  • Add tests function for atlas_seurat.py. [Christophe Bécavin]

  • Add all tests function for atlas.py. [Christophe Bécavin]

  • Create utils module with folders.py and files.py. [Christophe Bécavin]

  • Release: version 0.2.13 🚀 [Christophe Bécavin]

  • Mve argumentparser to checkatlas core, add tests functions for get_viable- functions in atlas.py. [Christophe Bécavin]

  • Start adding test function for atlas.py. [Christophe Bécavin]

  • Release: version 0.2.12 🚀 [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.12. [Christophe Bécavin]

  • Format and lint. [Christophe Bécavin]

  • Release: version 0.2.11 🚀 [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.11. [Christophe Bécavin]

  • Fromat and lint. [Christophe Bécavin]

  • Fix rpy2 to 3.5.10. [Christophe Bécavin]

  • Remove atlas-info from atlas_seurat, Downgrade rpy2 to 3.5.10 otherwise it crashes with 3.5.13. [Christophe Bécavin]

  • Remove all atlasinfo from atlas.py, clean all docstrings in atlas.py. [Christophe Bécavin]

  • Remove condainfo variable (obsolete) [Christophe Bécavin]

  • Remove condainfo variable (obsolete) [Christophe Bécavin]

  • Add all function and datasets for testing. [Christophe Bécavin]

  • Add all folders.py tests. [Christophe Bécavin]

  • Parse doc to gogle style in folders. [Christophe Bécavin]

  • Update README.md. [drbecavin]

    Add static badges

  • Release: version 0.2.10 🚀 [Christophe Bécavin]

  • Fix few things in the doc. [Christophe Bécavin]

  • Release: version 0.2.9 🚀 [Christophe Bécavin]

  • Add logo to doc, remove lint test on windows. [Christophe Bécavin]

  • Update README.md. [drbecavin]

  • Update README.md. [drbecavin]

    Add logo to readme

  • Update README.md. [drbecavin]

    Add lg to readme

  • Move logo. [Christophe Bécavin]

  • Release: version 0.2.8 🚀 [Christophe Bécavin]

  • Continuous integration 🔄 tests-0.2.8. [Christophe Bécavin]

  • Update index.md. [drbecavin]

    change index in doc with badges

  • Update README.md. [drbecavin]

    add bioconda badge

  • Update README.md. [drbecavin]

    fix gitter

  • Update README.md. [drbecavin]

    add pypi badge

  • Update pyproject.toml. [drbecavin]

    Change license in toml

  • Update README.md. [drbecavin]

    Add pypi license badge

  • Update README.md. [drbecavin]

    Add Pypi dl badge

  • Update README.md. [drbecavin]

    gitter badge

  • Update README.md. [drbecavin]

  • Update README.md. [drbecavin]

    add gitter badge

  • Release: version 0.2.7 🚀 [Christophe Bécavin]

  • Add poetry to dependencies (for bioconda) [Christophe Bécavin]

  • Fix minor bugs after separation of workflow. [Christophe Bécavin]

  • Release: version 0.2.6 🚀 [Christophe Bécavin]

  • Prepare for test release without workflow (all moved to nf-core- checkatlas) [Christophe Bécavin]

  • Remove dependecies nextflow, multiqc and clean toml project. [Christophe Bécavin]

  • Remove all files related to workflow; Moved them to nf-core- checkatlas. [Christophe Bécavin]

  • Create nfworkflow.py, and add all workflow related scrpts. [Christophe Bécavin]

  • Update LICENSE. [drbecavin]

    Change license to BSD

  • Merge pull request #37 from becavin-lab/multiqc. [drbecavin]

    Multiqc

  • Fix celllimit argument and QC tables export. [Christophe Bécavin]

  • Change the QC tables by adding directly rank of each cells for each QC metric (This was previously done in MultiQC) [Christophe Bécavin]

  • Add plot_celllimit argument for table export limit. In order to allow multiqc to manage the plots. [Christophe Bécavin]

  • Put back nextflow in main branch for MultiQC tests. [Christophe Bécavin]

  • Remove nextflow dependency. [Christophe Bécavin]

  • Format files, switch to VScode, remove .idea. [drbecavin]

  • Format files, switch to VScode, remove .idea. [drbecavin]

  • Release: version 0.2.2 🚀 [drbecavin]

  • Continuous integration 🔄 tests-0.2.2. [drbecavin]

  • Continuous integration 🔄 tests-0.2.1. [drbecavin]

  • Add first metrics docs, reorganize doc. [drbecavin]

  • Fiix readthedoc issue with R. [drbecavin]

  • Fiix readthedoc issue with R. [drbecavin]

  • Add poetry in the readthedoc workflow. [drbecavin]

  • Add poetry in the readthedoc workflow. [drbecavin]

  • Add poetry in the readthedoc workflow. [drbecavin]

  • Dependecy problem inb readthedoc. [drbecavin]

  • Add mkdocsstrings to autogenerate API doncs. Docstrings switch to google style. [drbecavin]

  • Add mkdocsstrings to autogenerate API doncs. Docstrings switch to google style. [drbecavin]

  • Add mkdocsstrings to autogenerate API doncs. Docstrings switch to google style. [drbecavin]

  • Add mkdocsstrings to autogenerate API doncs. Docstrings switch to google style. [drbecavin]

  • Add mkdocsstrings to autogenerate API doncs. Docstrings switch to google style. [drbecavin]

  • Add mkdocsstrings to autogenerate API doncs. Docstrings switch to google style. [drbecavin]

  • Add mkdocsstrings to autogenerate API doncs. Docstrings switch to google style. [drbecavin]

  • Add mkdocsstrings to autogenerate API doncs. Docstrings switch to google style. [drbecavin]

  • Add mkdocsstrings to autogenerate API doncs. Docstrings switch to google style. [drbecavin]

  • Add mkdocsstrings to autogenerate API doncs. Docstrings switch to google style. [drbecavin]

  • Modify docs. [drbecavin]

  • Release: version 0.2.1 🚀 [drbecavin]

  • Continuous integration 🔄 tests-0.2.1. [drbecavin]

  • Modify all metrics, each metric is in individual python file. One can add new metrics easily. [drbecavin]

  • Fix small import stuff. [drbecavin]

  • Release: version 0.2.0 🚀 [drbecavin]

  • Merge pull request #33 from becavin-lab/workflow. [drbecavin]

    Workflow

  • Move examples to docs/examples/ [drbecavin]

  • Continuous integration 🔄 tests-0.2.0. [drbecavin]

  • Release: version 0.1.23 🚀 [drbecavin]

  • Release: version 0.1.22 🚀 [drbecavin]

  • Fix total number of threads with -nextflow param. [drbecavin]

  • Fix total number of threads with -nextflow param. [drbecavin]

  • Fix total number of threads with -nextflow param. [drbecavin]

  • Fix total number of threads with -nextflow param. [drbecavin]

  • Add nextflow parameters for multithread or not. [drbecavin]

  • Release: version 0.1.21 🚀 [drbecavin]

  • Continuous integration 🔄 tests-0.1.21. [drbecavin]

  • Fix error in args.path being relative instead of absolute. [drbecavin]

  • Release: version 0.1.20 🚀 [drbecavin]

  • Continuous integration 🔄 tests-7. [drbecavin]

  • Continuous integration 🔄 tests-0.1.20. [drbecavin]

  • Add nextflow and remove flask to dependencies. [drbecavin]

  • First nextflow workflow added. [drbecavin]

  • Create checkatlas-workflow and run it with nextflow. [drbecavin]

  • Add summary table at end of workflow to improve resume function. [drbecavin]

  • Fix numpy conversion for umap and tsne reductions. [Christophe Bécavin]

  • Fix umap and tsne obsm search. [drbecavin]

  • Fix poetry lock with numpy 1.23.5. [drbecavin]

  • Fix umap and tsne obsm search. [drbecavin]

  • Fix umap obsm search. [drbecavin]

  • Fix umap obsm search. [drbecavin]

  • Fix makesunique for atlas cleaning. [drbecavin]

  • Fix makesunique for atlas cleaning. [drbecavin]

  • Fix makesunique for atlas cleaning. [drbecavin]

  • Fix makesunique for atlas cleaning. [drbecavin]

  • Ix raw.var_names not unique problem. [Christophe Bécavin]

  • Update poetry lock. [drbecavin]

  • Update poetry lock. [drbecavin]

  • Release: version 0.1.19 🚀 [drbecavin]

  • Modify docs. [drbecavin]

  • Modify readme. [drbecavin]

  • Release: version 0.1.18 🚀 [drbecavin]

  • Continuous integration 🔄 [drbecavin]

  • Continuous integration 🔄 [drbecavin]

  • Fix continuous integration with github workflow. [drbecavin]

  • Add tests workfllow file. [drbecavin]

  • Add tests workfllow file. [drbecavin]

  • Modify git tag management for release and docs. [drbecavin]

  • Release: version 0.1.17 🚀 [drbecavin]

  • Modify git tag management for release and docs. [drbecavin]

  • Update documentation. [drbecavin]

0.1.16 (2023-02-17)

  • Release: version 0.1.16 🚀 [drbecavin]

0.1.15 (2023-02-17)

  • Release: version 0.1.15 🚀 [drbecavin]

0.1.14 (2023-02-16)

  • Release: version 0.1.14 🚀 [drbecavin]
  • Release: version 0.1.13 🚀 [drbecavin]

0.1.13 (2023-02-16)

  • Release: version 0.1.13 🚀 [drbecavin]

0.1.12 (2023-02-16)

  • Release: version 0.1.12 🚀 [drbecavin]
  • Release: version 0.1.11 🚀 [drbecavin]
  • Modify release;yaml to get pypi publication running. [drbecavin]

0.1.11 (2023-02-16)

  • Release: version 0.1.11 🚀 [drbecavin]
  • Modify release;yaml to get pypi publication running. [drbecavin]
  • Release: version 0.1.10 🚀 [drbecavin]
  • Test pypi token. [drbecavin]

0.1.10 (2023-02-16)

  • Release: version 0.1.10 🚀 [drbecavin]

0.1.3 (2023-02-16)

  • Release: version 0.1.3 🚀 [drbecavin]
  • Release: version 🚀 [drbecavin]
  • Release: version 🚀 [drbecavin]

0.1.7 (2023-02-16)

  • Release: version 0.1.7 🚀 [drbecavin]

0.1.6 (2023-02-16)

  • Release: version 0.1.6 🚀 [drbecavin]

0.1.5 (2023-02-16)

  • Release: version 0.1.5 🚀 [drbecavin]
  • Release: version 0.1.4 🚀 [drbecavin]

0.1.4 (2023-02-16)

  • Release: version 0.1.4 🚀 [drbecavin]

  • Modify release workflow. [drbecavin]

  • Merge pull request #32 from becavin-lab/metrics. [drbecavin]

    Poetrry package manager added

  • Modify github workflow for tests. [drbecavin]

  • Modify github workflow for tests. [drbecavin]

  • Modify github workflow for tests. [drbecavin]

  • Add poetry for github workflow. [drbecavin]

  • Add poetry for github workflow. [drbecavin]

  • Add poetry for github workflow. [drbecavin]

  • Add poetry for github workflow. [drbecavin]

  • Add poetry for github workflow. [drbecavin]

  • After poetry add fix MakeFile. [drbecavin]

  • Switch to poetry. [drbecavin]

  • Fix var_names not unique. [drbecavin]

  • Fix var_names not unique. [drbecavin]

  • Branch metrics. [Christophe Bécavin]

  • Test git. [Christophe Bécavin]

  • Test git. [Christophe Bécavin]

  • Test. [Paola Porracciolo]

  • Test. [Paola Porracciolo]

0.1.2 (2022-07-29)

  • Release: version 0.1.2 🚀 [drbecavin]
  • Modify summary. [drbecavin]

0.1.1 (2022-07-29)

  • Release: version 0.1.1 🚀 [drbecavin]
  • Add examples to docs. [drbecavin]
  • Update checkatlas examples. [drbecavin]
  • Update checkatlas examples. [drbecavin]
  • Update doc. [drbecavin]
  • Update doc. [drbecavin]
  • Merge branch 'main' of github.com:becavin-lab/checkatlas Good. [drbecavin]
  • Update README.md. [drbecavin]
  • Update README.md. [drbecavin]
  • Update doc. [drbecavin]

0.1.0 (2022-07-29)

  • Release: version 0.1.0 🚀 [drbecavin]

  • Minor bug correction. [drbecavin]

  • Merge pull request #26 from becavin-lab/rpy2. [drbecavin]

    Rpy2

  • Minor bug correction. [drbecavin]

  • Fix requirements. [drbecavin]

  • Fix requirements. [drbecavin]

  • Fix requirements. [drbecavin]

  • Run lint, clean code. [drbecavin]

  • Add metrics calculation for Seurat objects (dimred not working yet) [drbecavin]

  • Implement Seurat management via rpy2. Summary, adata, qc and umap/tsne is now performed with R. No conversion from seurat to scanpy is needed anymore. [drbecavin]

  • Parse Cellranger files by searching for clustering and reductions in outs/analysis/ folder. [drbecavin]

  • Separate search of scanpy, seurat and cellranger. Add atlas_seurat for managing Seurat object with rpy2. [drbecavin]

  • Update README.md. [drbecavin]

0.0.16 (2022-07-26)

  • Release: version 0.0.16 🚀 [drbecavin]
  • Improve metrics management. Add annot and dimred metrics. [drbecavin]
  • Add Metrics management with arguments, you can specify now the metrics to run inside the argument list or usng config file. Fix also the use of config/default_config.yaml to specify program arguments. [drbecavin]

0.0.15 (2022-07-22)

  • Release: version 0.0.15 🚀 [drbecavin]
  • Replace print by logger.info and logger.debug. [drbecavin]

0.0.14 (2022-07-22)

  • Release: version 0.0.14 🚀 [drbecavin]
  • Add config file management for program arguments. [drbecavin]
  • Add parameters and logger in main. [drbecavin]

0.0.13 (2022-07-19)

  • Release: version 0.0.13 🚀 [drbecavin]
  • Add QC tables for Knee plots. [drbecavin]

0.0.12 (2022-07-08)

  • Release: version 0.0.12 🚀 [drbecavin]

0.0.11 (2022-07-08)

  • Release: version 0.0.11 🚀 [drbecavin]

0.0.10 (2022-07-08)

  • Release: version 0.0.10 🚀 [drbecavin]
  • Prepare QC table production. [drbecavin]
  • Test.txt. [drbecavin]
  • Change in workflow. [drbecavin]

0.0.9 (2022-06-20)

  • Release: version 0.0.9 🚀 [drbecavin]
  • Fix project release. [drbecavin]

0.0.8 (2022-06-20)

  • Release: version 0.0.8 🚀 [drbecavin]
  • Fix project release. [drbecavin]

0.0.7 (2022-06-20)

  • Release: version 0.0.7 🚀 [drbecavin]
  • Release: version 0.0.6 🚀 [drbecavin]

0.0.6 (2022-06-20)

  • Release: version 0.0.6 🚀 [drbecavin]
  • Clean docs. [drbecavin]
  • Update README.md. [drbecavin]
  • Modify readme docs. [drbecavin]
  • Update README.md. [drbecavin]

0.0.5 (2022-06-20)

  • Release: version 0.0.5 🚀 [drbecavin]

0.0.4 (2022-06-20)

  • Release: version 0.0.4 🚀 [drbecavin]
  • Modify readme docs. [drbecavin]
  • Update README.md. [drbecavin]
  • Add examples in the doc. [drbecavin]

0.0.3 (2022-06-18)

  • Release: version 0.0.3 🚀 [drbecavin]
  • Merge branch 'main' of github.com:becavin-lab/checkatlas good. [drbecavin]
  • Update README.md. [drbecavin]
  • Update README.md. [drbecavin]
  • Fix umap display. [drbecavin]
  • Fix category management in adata.obs. [drbecavin]
  • Add test on scanp version. [drbecavin]

0.0.2 (2022-06-16)

  • Release: version 0.0.2 🚀 [drbecavin]
  • Release: version 0.0.1 🚀 [drbecavin]
  • Fix release making. [drbecavin]
  • Merge branch 'main' of github.com:becavin-lab/checkatlas Good. [drbecavin]
  • Update README.md. [drbecavin]
  • Fix release making. [drbecavin]

0.0.1 (2022-06-16)

  • Release: version 0.0.1 🚀 [drbecavin]

  • Release: version 🚀 [drbecavin]

  • Release: version 🚀 [drbecavin]

  • Release: version 🚀 [drbecavin]

  • Release: version 🚀 [drbecavin]

  • Release: version 🚀 [drbecavin]

  • Clean project before release. [drbecavin]

  • Release: version 🚀 [drbecavin]

  • Add corrupted h5ad management with AnnDataReadError. [drbecavin]

  • Add corrupted h5ad management with AnnDataReadError. [drbecavin]

  • Add resume capacity in checkatlas.py. [drbecavin]

  • Fix obs_beys selection. [drbecavin]

  • Add list_atlases.csv. [drbecavin]

  • Fix list files. [drbecavin]

  • Add HLCA index names. [drbecavin]

  • Release: version 🚀 [drbecavin]

  • Clean project. [drbecavin]

  • Clean files. [drbecavin]

  • Remove rds from type of file. [christophe Becavin]

  • Prepare checkatlas for discovair. [christophe Becavin]

  • Clean all codes. make fmt, make lint, and make docs. [christophe Becavin]

  • Make fmt. [christophe Becavin]

  • Add read the docs conf. [christophe Becavin]

  • Add read the docs conf. [christophe Becavin]

  • Add read the docs conf. [christophe Becavin]

  • Add read the docs conf. [christophe Becavin]

  • Add read the docs conf. [christophe Becavin]

  • Add all examples. [christophe Becavin]

  • Add all examples. [christophe Becavin]

  • Update README.md. [drbecavin]

  • Update README.md. [drbecavin]

  • Add example 2 and 3. [christophe Becavin]

  • Add html examples. [christophe Becavin]

  • Merge branch 'main' of github.com:becavin-lab/checkatlas. [christophe Becavin]

  • Update README.md. [drbecavin]

  • Add html examples. [christophe Becavin]

  • Add Example 1 and 2. [christophe Becavin]

  • Add examples to checkatlas. [christophe Becavin]

  • Update README.md. [drbecavin]

  • Reformat code. [christophe Becavin]

  • #18 Add os.sep in filename, Put multihread=False by default. [christophe Becavin]

  • Close #18, add folders.py to save all files in checkatlas_files/ folder. [christophe Becavin]

  • Merge branch 'main' of github.com:becavin-lab/checkatlas. [christophe Becavin]

  • Update README.md. [drbecavin]

    Add summary

  • Add pycharm run configuration. [christophe Becavin]

  • First big update : Labmeeting presentation. Prototyp is ready. [christophe Becavin]

  • Add Antoine metrics, add Dask. [christophe Becavin]

  • Release: version 🚀 [christophe Becavin]

  • Reformat and lint corrected. [christophe Becavin]

  • Modifi atlas.py return statement. [christophe Becavin]

  • Merge branch 'main' of github.com:becavin-lab/checkatlas. [christophe Becavin]

  • Update README.md. [drbecavin]

  • Add files for github workflow and template. [christophe Becavin]

  • Clean project files. [christophe Becavin]

  • Remove github templates from project creation. [christophe Becavin]

  • Add git ignore. [christophe Becavin]

  • Add git ignore. [christophe Becavin]

  • ✅ Ready to clone and code. [drbecavin]

  • First commit with many changes. [christophe Becavin]

  • Initial commit. [drbecavin]