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@@ -21,3 +21,4 @@ R/flippitise.R | |
| ^playground | ||
| ^doc$ | ||
| ^Meta$ | ||
| ^codecov\.yml$ | ||
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: [main, master] | ||
| pull_request: | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
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| name: pkgdown.yaml | ||
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| permissions: read-all | ||
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| jobs: | ||
| pkgdown: | ||
| runs-on: ubuntu-latest | ||
| # Only restrict concurrency for non-PR jobs | ||
| concurrency: | ||
| group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| permissions: | ||
| contents: write | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
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| - uses: r-lib/actions/setup-pandoc@v2 | ||
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| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
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| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::pkgdown, local::. | ||
| needs: website | ||
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| - name: Build site | ||
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | ||
| shell: Rscript {0} | ||
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| - name: Deploy to GitHub pages 🚀 | ||
| if: github.event_name != 'pull_request' | ||
| uses: JamesIves/[email protected] | ||
| with: | ||
| clean: false | ||
| branch: gh-pages | ||
| folder: docs |
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| @@ -1,57 +1,51 @@ | ||
| url: "https://bioinformatics.mdc-berlin.de/anglemania" | ||
| url: http://bioinformatics.mdc-berlin.de/anglemania/ | ||
| template: | ||
| bootstrap: 5 | ||
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| reference: | ||
| - title: Main | ||
| desc: > | ||
| The two functions for running anglemania. | ||
| contents: | ||
| - create_anglemania_object | ||
| - anglemania | ||
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| - title: Computation of Statistics | ||
| desc: > | ||
| Functions that work behind the scenes of anglemania to get the statistics. | ||
| contents: | ||
| - factorise | ||
| - extract_angles | ||
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| - title: Utilities | ||
| desc: > | ||
| anglemania utilities. | ||
| contents: | ||
| - sparse_to_fbm | ||
| - get_dstat | ||
| - big_mat_list_mean | ||
| - get_list_stats | ||
| - extract_rows_for_unique_genes | ||
| - select_genes | ||
| - integrate_by_features | ||
| - integrate_seurat_list | ||
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| - title: Anglem Object Helpers | ||
| desc: > | ||
| Helper functions to access and set anglem object attributes. | ||
| contents: | ||
| - anglemania_object-class | ||
| - matrix_list | ||
| - "matrix_list<-" | ||
| - dataset_key | ||
| - batch_key | ||
| - data_info | ||
| - angl_weights | ||
| - "angl_weights<-" | ||
| - list_stats | ||
| - "list_stats<-" | ||
| - intersect_genes | ||
| - "intersect_genes<-" | ||
| - get_anglemania_genes | ||
| - add_unique_batch_key | ||
|
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||
| - title: Main | ||
| desc: | | ||
| The two functions for running anglemania. | ||
| contents: | ||
| - create_anglemania_object | ||
| - anglemania | ||
| - title: Computation of Statistics | ||
| desc: | | ||
| Functions that work behind the scenes of anglemania to get the statistics. | ||
| contents: | ||
| - factorise | ||
| - extract_angles | ||
| - title: Utilities | ||
| desc: | | ||
| anglemania utilities. | ||
| contents: | ||
| - sparse_to_fbm | ||
| - get_dstat | ||
| - big_mat_list_mean | ||
| - get_list_stats | ||
| - extract_rows_for_unique_genes | ||
| - select_genes | ||
| - integrate_by_features | ||
| - integrate_seurat_list | ||
| - title: Anglem Object Helpers | ||
| desc: | | ||
| Helper functions to access and set anglem object attributes. | ||
| contents: | ||
| - anglemania_object-class | ||
| - matrix_list | ||
| - matrix_list<- | ||
| - dataset_key | ||
| - batch_key | ||
| - data_info | ||
| - angl_weights | ||
| - angl_weights<- | ||
| - list_stats | ||
| - list_stats<- | ||
| - intersect_genes | ||
| - intersect_genes<- | ||
| - get_anglemania_genes | ||
| - add_unique_batch_key | ||
| articles: | ||
| - title: "Articles" | ||
| navbar: ~ | ||
| contents: | ||
| - "anglemania_tutorial" | ||
| - title: Articles | ||
| navbar: ~ | ||
| contents: anglemania_tutorial | ||
|
|
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| comment: false | ||
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| coverage: | ||
| status: | ||
| project: | ||
| default: | ||
| target: auto | ||
| threshold: 1% | ||
| informational: true | ||
| patch: | ||
| default: | ||
| target: auto | ||
| threshold: 1% | ||
| informational: true |