Files in ChromSCape
Analysis of single-cell epigenomics datasets with a Shiny App
.BBSoptions
README.md
NEWS
NAMESPACE
DESCRIPTION
build/vignette.rds
data/mm10.GeneTSS.rda
data/scExp.rda
data/hg38.GeneTSS.rda
data/hg38.chromosomes.rda
data/mm10.chromosomes.rda
R/runApp.R
R/moreImports.R
R/plotting_functions.R
R/zzz.R
R/preprocessing_filtering_reduction.R
R/support_functions.R
R/data.R
R/peak_calling.R
R/diff_analysis_gene_set_enrichment.R
R/correlation_filtering_clustering.R
vignettes/vignette.Rmd
longtests/testthat.R
longtests/testthat/test_correlation_clustering.R
longtests/testthat/test_processing_filtering.R
longtests/testthat/test_diff_analysis_gene_set_enrichment.R
man/run_pairwise_tests.Rd
man/DA_one_vs_rest_fun.Rd
man/index_peaks_barcodes_to_matrix_indexes.Rd
man/generate_feature_names.Rd
man/mm10.GeneTSS.Rd
man/call_macs2_merge_peaks.Rd
man/DA_pairwise.Rd
man/filter_scExp.Rd
man/combine_datamatrix.Rd
man/anocol_binary.Rd
man/preprocess_feature_size_only.Rd
man/remove_chr_M_fun.Rd
man/preprocess_CPM.Rd
man/normalize_scExp.Rd
man/read_count_mat_with_separated_chr_start_end.Rd
man/num_cell_after_cor_filt_scExp.Rd
man/peaks_to_bins.Rd
man/has_genomic_coordinates.Rd
man/separator_count_mat.Rd
man/run_tsne_scExp.Rd
man/choose_perplexity.Rd
man/pca_irlba_for_sparseMatrix.Rd
man/plot_cluster_consensus_scExp.Rd
man/detect_samples.Rd
man/preprocess_TPM.Rd
man/distPearson.Rd
man/reduce_dims_scExp.Rd
man/generate_count_matrix.Rd
man/load_MSIGdb.Rd
man/consensus_clustering_scExp.Rd
man/plot_heatmap_scExp.Rd
man/anocol_categorical.Rd
man/remove_non_canonical_fun.Rd
man/create_sample_name_mat.Rd
man/plot_reduced_dim_scExp.Rd
man/results_enrichmentTest.Rd
man/num_cell_after_QC_filt_scExp.Rd
man/plot_distribution_scExp.Rd
man/gg_fill_hue.Rd
man/beds_to_matrix_indexes.Rd
man/plot_differential_volcano_scExp.Rd
man/plot_differential_summary_scExp.Rd
man/separate_BAM_into_clusters.Rd
man/import_count_input_files.Rd
man/correlation_and_hierarchical_clust_scExp.Rd
man/warning_DA.Rd
man/reduce_dim_batch_correction.Rd
man/choose_cluster_scExp.Rd
man/num_cell_scExp.Rd
man/annotation_from_merged_peaks.Rd
man/annotToCol2.Rd
man/warning_raw_counts_to_feature_count_files.Rd
man/enrichmentTest.Rd
man/bams_to_matrix_indexes.Rd
man/groupMat.Rd
man/get_color_dataframe_from_input.Rd
man/colors_scExp.Rd
man/mm10.chromosomes.Rd
man/gene_set_enrichment_analysis_scExp.Rd
man/warning_filter_correlated_cell_scExp.Rd
man/warning_plot_reduced_dim_scExp.Rd
man/merge_MACS2_peaks.Rd
man/subsample_scExp.Rd
man/col2hex.Rd
man/get_genomic_coordinates.Rd
man/define_feature.Rd
man/create_scDataset_raw.Rd
man/num_cell_in_cluster_scExp.Rd
man/feature_annotation_scExp.Rd
man/check_correct_datamatrix.Rd
man/import_scExp.Rd
man/changeRange.Rd
man/launchApp.Rd
man/preprocess_RPKM.Rd
man/hg38.chromosomes.Rd
man/filter_genes_with_refined_peak_annotation.Rd
man/table_enriched_genes_scExp.Rd
man/subset_bam_call_peaks.Rd
man/hclustAnnotHeatmapPlot.Rd
man/filter_correlated_cell_scExp.Rd
man/hg38.GeneTSS.Rd
man/num_cell_before_cor_filt_scExp.Rd
man/CompareWilcox.Rd
man/raw_counts_to_feature_count_files.Rd
man/exclude_features_scExp.Rd
man/imageCol.Rd
man/plot_differential_H1_scExp.Rd
man/H1proportion.Rd
man/combine_enrichmentTests.Rd
man/differential_analysis_scExp.Rd
man/create_scExp.Rd
man/CompareedgeRGLM.Rd
man/scExp.Rd
tests/testthat.R
tests/testthat/test_default_run.R
inst/app.js
inst/ui.R
inst/intro.min.js
inst/Module_preprocessing_filtering_and_reduction.R
inst/server.R
inst/js.cookie.js
inst/doc/vignette.html
inst/doc/vignette.R
inst/doc/vignette.Rmd
inst/www/curie.jpg
inst/www/app.js
inst/www/app.css
inst/www/shiny_js_functions.js
inst/www/intro.min.js
inst/www/introjs.min.css
inst/www/style.css
inst/www/ChromSCape_concept.png
inst/www/Guide_images/Step7_GeneSetAnalysis.png
inst/www/Guide_images/Step4_1_cluster_cells.png
inst/www/Guide_images/Step1_select_import.png
inst/www/Guide_images/Step6_DA.png
inst/www/Guide_images/Step3_visualize_cells.png
inst/www/Guide_images/Step2_filter_normalize.png
inst/www/Guide_images/Step1_format_input.png
inst/www/Guide_images/Step4_table_UMAP.png
inst/www/Guide_images/Step5_peak_calling.png
inst/www/helpfiles/datamatrix_input.md
inst/www/helpfiles/consensus_clustering.md
inst/www/helpfiles/filter_correlation_distrib.md
inst/www/helpfiles/umap_plot.md
inst/www/helpfiles/output_directory.md
inst/www/helpfiles/exclude_region.md
inst/www/helpfiles/run_tsne.md
inst/www/helpfiles/ChromSCape.md
inst/www/helpfiles/tsne_plot.md
inst/www/helpfiles/batch_correction.md
inst/www/helpfiles/distrib_norm_hist.md
inst/www/helpfiles/subsampling.md
inst/www/helpfiles/choose_cluster.md
inst/www/helpfiles/filtering_parameters.md
inst/www/helpfiles/pca_plot.md
inst/www/helpfiles/consensus_association_heatmap.md
inst/www/helpfiles/correlation_clustering.md
