diff --git a/.Rbuildignore b/.Rbuildignore index f4666dc..b751679 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -2,13 +2,8 @@ ^renv\.lock$ ^.*\.Rproj$ ^\.Rproj\.user$ -^cleanup -\.jpg$ ^anglemania\.Rproj$ .Rprofile -explore_function_scape.R -functions_graph.svg -R/flippitise.R ^vignettes$ ^LICENSE\.md$ ^\.github$ @@ -17,9 +12,8 @@ R/flippitise.R ^_pkgdown\.yml$ ^docs$ ^pkgdown$ -^tmp_bm ^playground ^doc$ ^Meta$ ^codecov\.yml$ -^.vsode \ No newline at end of file +^.vscode \ No newline at end of file diff --git a/._.DS_Store b/._.DS_Store deleted file mode 100755 index c3bcf45..0000000 Binary files a/._.DS_Store and /dev/null differ diff --git a/._pkgdown.yml.swp b/._pkgdown.yml.swp deleted file mode 100644 index 7d71f3d..0000000 Binary files a/._pkgdown.yml.swp and /dev/null differ diff --git a/800px-Tissot_The_Gathering_of_the_Manna_(color).jpg b/800px-Tissot_The_Gathering_of_the_Manna_(color).jpg deleted file mode 100644 index 5f0ac27..0000000 Binary files a/800px-Tissot_The_Gathering_of_the_Manna_(color).jpg and /dev/null differ diff --git a/_pkgdown.yml b/_pkgdown.yml deleted file mode 100644 index 1e9b46e..0000000 --- a/_pkgdown.yml +++ /dev/null @@ -1,51 +0,0 @@ -url: http://bioinformatics.mdc-berlin.de/anglemania/ -template: - bootstrap: 5 -reference: -- 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 - 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``` # Normal anglemania workflow diff --git a/vignettes/anglemania_tutorial_SCE.Rmd b/vignettes/anglemania_tutorial_SCE.Rmd index 822a917..e1f9fa1 100644 --- a/vignettes/anglemania_tutorial_SCE.Rmd +++ b/vignettes/anglemania_tutorial_SCE.Rmd @@ -31,8 +31,7 @@ anglemania can be used on top of SingleCellExperiment or Seurat objects. ```{r, load libraries} suppressPackageStartupMessages({ - # library(anglemania) - devtools::load_all() + library(anglemania) library(dplyr) library(Seurat) library(splatter) diff --git a/vignettes/anglemania_tutorial_Seurat.Rmd b/vignettes/anglemania_tutorial_Seurat.Rmd index c8ef953..355fbb4 100644 --- a/vignettes/anglemania_tutorial_Seurat.Rmd +++ b/vignettes/anglemania_tutorial_Seurat.Rmd @@ -31,8 +31,7 @@ anglemania can be used on top of SingleCellExperiment or Seurat objects. ```{r, load libraries} suppressPackageStartupMessages({ - devtools::load_all() - # library(anglemania) + library(anglemania) library(dplyr) library(Seurat) library(splatter)