Files in saeyslab/muscatWrapper
Wrapper functions around muscat for differential expression analysis of multi-sample multi-condition scRNAseq datasets
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
R-raw/add_data.R
R/data.R
R/expression_processing.R
R/muscat_de.R
R/pipeline.R
R/pipeline_wrappers.R
R/plotting.R
README.Rmd
README.md
data/sce.rda
man/add_empirical_pval_fdr.Rd
man/fix_frq_df.Rd
man/get_DE_info.Rd
man/get_FDR_empirical.Rd
man/get_FDR_empirical_plots.Rd
man/get_FDR_empirical_plots_all.Rd
man/get_abundance_info.Rd
man/get_avg_frac_exprs_abund.Rd
man/get_empirical_pvals.Rd
man/get_expression_info.Rd
man/get_muscat_exprs_avg.Rd
man/get_muscat_exprs_frac.Rd
man/get_pseudobulk_logCPM_exprs.Rd
man/make_DEgene_dotplot_pseudobulk.Rd
man/make_DEgene_dotplot_pseudobulk_covariate.Rd
man/make_DEgene_dotplot_pseudobulk_reversed.Rd
man/make_DEgene_violin_plot.Rd
man/muscat_analysis.Rd
man/p.adjust_empirical.Rd
man/perform_muscat_de_analysis.Rd
man/sce.Rd
muscatWrapper.Rproj
tests/test_pipeline.R
tests/testthat/test-pipeline.R
vignettes/basic_analysis.Rmd
vignettes/basic_analysis.html
vignettes/basic_analysis.md
vignettes/basic_analysis_batchcor.Rmd
vignettes/basic_analysis_batchcor.html
vignettes/basic_analysis_batchcor.md
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-10-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-104-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-105-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-106-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-107-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-108-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-109-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-15-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-17-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-18-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-18-2.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-2-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-2-2.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-2-3.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-2-4.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-27-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-28-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-29-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-3-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-30-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-31-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-32-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-79-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-79-2.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-79-3.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-79-4.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-8-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-80-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-85-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-86-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-87-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-9-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-92-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-94-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-95-1.png
vignettes/basic_analysis_batchcor_files/figure-gfm/unnamed-chunk-95-2.png
vignettes/basic_analysis_empnull.Rmd
vignettes/basic_analysis_empnull.html
vignettes/basic_analysis_empnull.md
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-14-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-17-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-18-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-18-2.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-18-3.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-18-4.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-18-5.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-18-6.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-19-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-19-2.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-19-3.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-19-4.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-19-5.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-19-6.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-2-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-2-2.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-2-3.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-2-4.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-21-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-22-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-22-2.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-23-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-23-2.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-30-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-30-2.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-30-3.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-30-4.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-35-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-36-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-37-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-42-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-45-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-46-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-46-2.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-46-3.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-46-4.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-46-5.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-46-6.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-47-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-47-2.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-47-3.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-47-4.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-47-5.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-47-6.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-49-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-50-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-50-2.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-7-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-8-1.png
vignettes/basic_analysis_empnull_files/figure-gfm/unnamed-chunk-9-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-14-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-16-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-17-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-17-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-18-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-18-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-2-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-2-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-2-3.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-2-4.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-35-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-35-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-35-3.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-35-4.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-40-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-40-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-40-3.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-40-4.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-41-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-42-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-45-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-46-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-47-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-49-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-50-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-50-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-51-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-51-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-52-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-53-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-53-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-54-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-55-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-55-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-56-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-56-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-58-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-60-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-61-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-61-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-63-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-64-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-64-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-64-3.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-64-4.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-69-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-7-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-70-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-71-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-76-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-78-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-79-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-79-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-8-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-80-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-80-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-82-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-82-2.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-84-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-87-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-89-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-9-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-90-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-92-1.png
vignettes/basic_analysis_files/figure-gfm/unnamed-chunk-93-1.png
vignettes/library.bib
vignettes/visualization_preparation.Rmd
vignettes/visualization_preparation.html
vignettes/visualization_preparation.md
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-12-1.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-12-2.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-12-3.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-12-4.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-17-1.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-18-1.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-18-2.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-2-1.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-2-2.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-2-3.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-2-4.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-7-1.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-8-1.png
vignettes/visualization_preparation_files/figure-gfm/unnamed-chunk-8-2.png
