Files in compbiomed/BatchQC

Batch Effects Quality Control Software

LICENSE.md NEWS.md R/Normalization.R R/batch_correction.R R/color_palette.R R/covariates_not_confounded.R R/data.R R/dendrogram.R R/dendrogram_alpha_numeric_check.R R/dendrogram_color_palette.R R/differential_expression.R R/explained_variation.R R/global_vars.R R/heatmap.R R/heatmap_num_to_char_convertor.R R/import.R R/negative_binomial_check.R R/pca.R R/preprocess.R R/runApp.R R/summary_statistics.R R/variation_ratios.R R/volcano_plot.R README.Rmd README.md inst/shiny/app.R inst/shiny/server/server_01_upload.R inst/shiny/server/server_02_experimentalDesign.R inst/shiny/server/server_03_variationAnalysis.R inst/shiny/server/server_04_heatmap.R inst/shiny/server/server_05_dendrogram.R inst/shiny/server/server_06_pca.R inst/shiny/server/server_07_differentialExpression.R inst/shiny/ui/ui_01_upload.R inst/shiny/ui/ui_02_experimental_design.R inst/shiny/ui/ui_03_variation.R inst/shiny/ui/ui_04_median_correlations.R inst/shiny/ui/ui_05_heatmaps.R inst/shiny/ui/ui_06_dendrogram.R inst/shiny/ui/ui_07_pca.R inst/shiny/ui/ui_08_shape.R inst/shiny/ui/ui_09_differential_expression_analysis.R inst/shiny/ui/ui_10_data_download.R inst/shiny/utils/helpers.R man/BatchQC.Rd man/DE_analyze.Rd man/EV_plotter.Rd man/EV_table.Rd man/PCA_plotter.Rd man/batch_correct.Rd man/batch_design.Rd man/batch_indicator.Rd man/batchqc_explained_variation.Rd man/bladder_data_upload.Rd man/check_valid_input.Rd man/color_palette.Rd man/combat_correction.Rd man/combat_seq_correction.Rd man/confound_metrics.Rd man/cor_props.Rd man/counts2pvalue.Rd man/covariates_not_confounded.Rd man/cramers_v.Rd man/dendrogram_alpha_numeric_check.Rd man/dendrogram_color_palette.Rd man/dendrogram_plotter.Rd man/get.res.Rd man/goodness_of_fit_DESeq2.Rd man/heatmap_num_to_char_converter.Rd man/heatmap_plotter.Rd man/nb_histogram.Rd man/nb_proportion.Rd man/normalize_SE.Rd man/plot_data.Rd man/preprocess.Rd man/process_dendrogram.Rd man/protein_data.Rd man/protein_sample_info.Rd man/pval_plotter.Rd man/pval_summary.Rd man/ratio_plotter.Rd man/signature_data.Rd man/std_pearson_corr_coef.Rd man/summarized_experiment.Rd man/variation_ratios.Rd man/volcano_plot.Rd tests/spelling.R tests/testthat.R tests/testthat/test-lintr.R vignettes/BatchQC_Intro.Rmd vignettes/BatchQC_examples.Rmd