diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index c7000b6..44e9f15 100755 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -19,6 +19,8 @@ jobs: - name: Build Documentation working-directory: docs run: sphinx-build . _build + - name: copy image files + run: cp -r docs/assets docs/_build/assets/ - uses: actions/upload-pages-artifact@v3 with: name: github-pages diff --git a/docs/count.md b/docs/count.md index 68c9ef7..7400cba 100755 --- a/docs/count.md +++ b/docs/count.md @@ -18,7 +18,7 @@ bean count --R1 R1.fq --R2 R2.fq -b A -f sgRNA_info_table.csv -r ``` By default, `bean count[-samples]` assume R1 and R2 are trimmed off of the adapter sequence. You may need to adjust the command arguments according to your read structure. - Read structuren + Read structuren See full detail [below](#full-parameters). diff --git a/docs/filter.md b/docs/filter.md index 4a04745..e05373d 100755 --- a/docs/filter.md +++ b/docs/filter.md @@ -16,7 +16,7 @@ You may want to adjust the flitering parameters to obtain optimal balance betwee # Translating alleles If you want to obtain **amino acid level variant** for coding sequence tiling screens, provide coding sequence positions which variants occuring within the coding sequence will be translated. *This is optional, but **highly recommended** to increase per-(coding)variant support.* -Allele translation +Allele translation ```bash diff --git a/docs/ldl_cds.md b/docs/ldl_cds.md index e2d5ce0..8b0379f 100755 --- a/docs/ldl_cds.md +++ b/docs/ldl_cds.md @@ -4,11 +4,11 @@ Tiling screen that tiles gRNA densely across locus or multiple loci, selected ba - + - +
Library designTiling (gRNAs tile each locus densely)
tiling library design 		Tiling (gRNAs tile each locus densely)
tiling library design
SelectionCells are sorted based on FACS signal quantiles
variant library design		Cells are sorted based on FACS signal quantiles
variant library design
diff --git a/docs/ldl_var.md b/docs/ldl_var.md index cdbf869..7eb1af7 100755 --- a/docs/ldl_var.md +++ b/docs/ldl_var.md @@ -1,14 +1,14 @@ -# Variant sorting screen tutorial +## Variant sorting screen tutorial GWAS variant screen with per-variant gRNA tiling design, selected based on FACS signal quantiles. - + - +
Library designVariant (gRNAs tile each target variant)
variant library design		Variant (gRNAs tile each target variant)
variant library design
SelectionCells are sorted based on FACS signal quantiles
variant library design		Cells are sorted based on FACS signal quantiles
variant library design
diff --git a/docs/profile.md b/docs/profile.md index 0300c16..cd40cb4 100755 --- a/docs/profile.md +++ b/docs/profile.md @@ -5,4 +5,4 @@ bean profile my_sorting_screen.h5ad -o output_prefix `# Prefix for editing profi # Output Above command produces `prefix_editing_preference.[html,ipynb]` as editing preferences ([see example](../notebooks/profile_editing_preference.ipynb)). -Allele translation \ No newline at end of file +Allele translation \ No newline at end of file diff --git a/docs/prolif_gwas.md b/docs/prolif_gwas.md index 3cac063..9af45ee 100644 --- a/docs/prolif_gwas.md +++ b/docs/prolif_gwas.md @@ -1,14 +1,14 @@ -# Variant sorting screen tutorial +## Variant survival screen tutorial GWAS variant screen with per-variant gRNA tiling design, selected based on FACS signal quantiles. - + - +
Library designVariant (gRNAs tile each target variant)
variant library design		Variant (gRNAs tile each target variant)
variant library design
SelectionCells are sorted based on FACS signal quantiles
variant library design		Cells are sorted based on FACS signal quantiles
variant library design
diff --git a/docs/prolif_gwas.rst b/docs/prolif_gwas.rst index 35d4175..2bdfa6b 100644 --- a/docs/prolif_gwas.rst +++ b/docs/prolif_gwas.rst @@ -1,4 +1,4 @@ -GWAS variant library +Proliferation screen with GWAS library *********************** .. mdinclude:: profile_gwas.md diff --git a/docs/qc.md b/docs/qc.md index ce85c44..ee89c3e 100755 --- a/docs/qc.md +++ b/docs/qc.md @@ -17,7 +17,7 @@ bean qc \ `bean qc` supports following quality control and masks samples with low quality. Specifically: -Allele translation +Allele translation * Plots guide coverage and the uniformity of coverage * Guide count correlation between samples diff --git a/docs/reporterscreen.md b/docs/reporterscreen.md index 0450470..03ce056 100644 --- a/docs/reporterscreen.md +++ b/docs/reporterscreen.md @@ -1,6 +1,6 @@ BEAN stores mapped gRNA and allele counts in `ReporterScreen` object which is compatible with [AnnData](https://anndata.readthedocs.io/en/latest/index.html). -ReporterScreen object structure +ReporterScreen object structure * `.guides`: guide information provided in input (`gRNA_library.csv` in above example) * `.samples`: sample information provided in input (`sample_list.csv` in above example) diff --git a/docs/run.md b/docs/run.md index c1de5bf..b0a478c 100755 --- a/docs/run.md +++ b/docs/run.md @@ -6,7 +6,7 @@ BEAN uses Bayesian network to incorporate gRNA editing outcome to provide poster For the full detail, see the method section of the [BEAN manuscript](https://www.medrxiv.org/content/10.1101/2023.09.08.23295253v1). -model +model

@@ -45,7 +45,7 @@ See full list of parameters [below](#full-parameters). # Output -model +model Above command produces * `output_prefix/bean_element_result.[model_type].csv` with following columns: diff --git a/docs/tutorials/ldl_cds.md b/docs/tutorials/ldl_cds.md index e2d5ce0..8b0379f 100755 --- a/docs/tutorials/ldl_cds.md +++ b/docs/tutorials/ldl_cds.md @@ -4,11 +4,11 @@ Tiling screen that tiles gRNA densely across locus or multiple loci, selected ba - + - +
Library designTiling (gRNAs tile each locus densely)
tiling library design 		Tiling (gRNAs tile each locus densely)
tiling library design
SelectionCells are sorted based on FACS signal quantiles
variant library design		Cells are sorted based on FACS signal quantiles
variant library design
diff --git a/docs/tutorials/ldl_var.md b/docs/tutorials/ldl_var.md index cdbf869..7eb1af7 100755 --- a/docs/tutorials/ldl_var.md +++ b/docs/tutorials/ldl_var.md @@ -1,14 +1,14 @@ -# Variant sorting screen tutorial +## Variant sorting screen tutorial GWAS variant screen with per-variant gRNA tiling design, selected based on FACS signal quantiles. - + - +
Library designVariant (gRNAs tile each target variant)
variant library design		Variant (gRNAs tile each target variant)
variant library design
SelectionCells are sorted based on FACS signal quantiles
variant library design		Cells are sorted based on FACS signal quantiles
variant library design