Update site with note on Bioconductor package bugs

Townsend-Lab-Yale · Oct 15, 2024 · db2fc05 · db2fc05
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diff --git a/NEWS.md b/NEWS.md
@@ -1,10 +1,10 @@
 
 # <font style = "opacity:0">cancereffectsizeR 3.0.0</font>
 Patch releases (as in, x.y.1 &#8594; x.y.2) have minor bug fixes or small improvements that do not significantly affect the numerical output of cancer effect analyses. Minor/major updates may change some outputs due to bug fixes or methodological tweaks, as described in these version notes.<br><br>
+
 # cancereffectsizeR 2.10.1
 * Minor fixes.
 
-
 # cancereffectsizeR 2.10.0
 * Tweaked optimizer settings for epistatic inference to improve convergence.
 * Added an initial version of an epistatic effect plotting function, plot_epistasis().

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/MAF_filtering_tips.html b/docs/articles/MAF_filtering_tips.html
diff --git a/docs/articles/cancereffectsizeR.html b/docs/articles/cancereffectsizeR.html
diff --git a/docs/articles/cosmic_cancer_type_note.html b/docs/articles/cosmic_cancer_type_note.html
diff --git a/docs/articles/create_custom_covariates.html b/docs/articles/create_custom_covariates.html
diff --git a/docs/articles/custom_refset_instructions.html b/docs/articles/custom_refset_instructions.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 3.1.11
+pandoc: '3.2'
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
@@ -7,7 +7,7 @@ articles:
   create_custom_covariates: create_custom_covariates.html
   custom_refset_instructions: custom_refset_instructions.html
   MAF_filtering_tips: MAF_filtering_tips.html
-last_built: 2024-07-08T17:57Z
+last_built: 2024-10-15T20:51Z
 urls:
   reference: https://townsend-lab-yale.github.io/cancereffectsizeR/reference
   article: https://townsend-lab-yale.github.io/cancereffectsizeR/articles

diff --git a/docs/reference/CESAnalysis.html b/docs/reference/CESAnalysis.html
diff --git a/docs/reference/CompoundVariantSet.html b/docs/reference/CompoundVariantSet.html
diff --git a/docs/reference/aac_to_snv_ids.html b/docs/reference/aac_to_snv_ids.html
diff --git a/docs/reference/add_covered_regions.html b/docs/reference/add_covered_regions.html
diff --git a/docs/reference/add_variants.html b/docs/reference/add_variants.html
diff --git a/docs/reference/annotate_variants.html b/docs/reference/annotate_variants.html
diff --git a/docs/reference/artifact_account.html b/docs/reference/artifact_account.html
diff --git a/docs/reference/assign_gr_to_coverage.html b/docs/reference/assign_gr_to_coverage.html
diff --git a/docs/reference/assign_group_average_trinuc_rates.html b/docs/reference/assign_group_average_trinuc_rates.html
diff --git a/docs/reference/baseline_mutation_rates.html b/docs/reference/baseline_mutation_rates.html
diff --git a/docs/reference/build_RefCDS.html b/docs/reference/build_RefCDS.html
diff --git a/docs/reference/calculate_trinuc_rates.html b/docs/reference/calculate_trinuc_rates.html
diff --git a/docs/reference/ces_epistasis.html b/docs/reference/ces_epistasis.html
diff --git a/docs/reference/ces_gene_epistasis.html b/docs/reference/ces_gene_epistasis.html