Files in vallotlab/ChromSCape
Analysis of single-cell epigenomics datasets with a Shiny App

.BBSoptions

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/RcppExports.R R/copy_number.R R/correlation_filtering_clustering.R R/coverage.R R/data.R R/diff_analysis_gene_set_enrichment.R R/generate_analysis.R R/init.R R/moreImports.R R/peak_calling.R R/plotting_functions.R R/preprocessing_filtering_reduction.R R/runApp.R R/support_functions.R R/zzz.R README.md

_pkgdown.yml

data/CheA3_TF_nTargets.rda

data/ce11.GeneTSS.rda

data/ce11.chromosomes.rda

data/hg38.GeneTSS.rda

data/hg38.chromosomes.rda

data/hg38.cytoBand.rda

data/mm10.GeneTSS.rda

data/mm10.chromosomes.rda

data/mm10.cytoBand.rda

data/scExp.rda

docs/404.html

docs/articles/index.html

docs/articles/scCutTag_Bartosovic_H3K27me3.html

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-10-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-11-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-12-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-13-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-15-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-16-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-18-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-19-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-5-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-6-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-7-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/figure-html/unnamed-chunk-8-1.png

docs/articles/scCutTag_Bartosovic_H3K27me3_files/header-attrs-2.8/header-attrs.js

docs/articles/scCutTag_Bartosovic_H3K27me3_files/kePrint-0.0.1/kePrint.js

docs/articles/scCutTag_Bartosovic_H3K27me3_files/lightable-0.0.1/lightable.css

docs/articles/vignette.html

docs/articles/vignette_files/header-attrs-2.8/header-attrs.js

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/inst/www/ChromSCape_concept.png

docs/inst/www/Guide_images/Step1_format_input.png

docs/inst/www/Guide_images/Step1_select_import.png

docs/inst/www/Guide_images/Step2_filter_normalize.png

docs/inst/www/Guide_images/Step3_UMAP.png

docs/inst/www/Guide_images/Step3_contribution_to_PCA.png

docs/inst/www/Guide_images/Step3_visualize_cells.png

docs/inst/www/Guide_images/Step4_1_cluster_cells.png

docs/inst/www/Guide_images/Step4_UMAP.png

docs/inst/www/Guide_images/Step4_intracorrelation.png

docs/inst/www/Guide_images/Step4_table_UMAP.png

docs/inst/www/Guide_images/Step5_peak_calling.png

docs/inst/www/Guide_images/Step6_DA.png

docs/inst/www/Guide_images/Step7_GeneSetAnalysis.png

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/CompareWilcox.html

docs/reference/CompareedgeRGLM.html

docs/reference/DA_custom.html

docs/reference/DA_one_vs_rest_fun.html

docs/reference/DA_pairwise.html

docs/reference/H1proportion.html

docs/reference/Rplot001.png

docs/reference/Rplot002.png

docs/reference/Rplot003.png

docs/reference/Rplot004.png

docs/reference/Rplot005.png

docs/reference/Rplot006.png

docs/reference/Rplot007.png

docs/reference/Rplot008.png

docs/reference/Rplot009.png

docs/reference/Rplot010.png

docs/reference/Rplot011.png

docs/reference/Rplot012.png

docs/reference/Rplot013.png

docs/reference/Rplot014.png

docs/reference/Rplot015.png

docs/reference/Rplot016.png

docs/reference/Rplot017.png

docs/reference/annotToCol2.html

docs/reference/annotation_from_merged_peaks.html

docs/reference/anocol_binary.html

docs/reference/anocol_categorical.html

docs/reference/bams_to_matrix_indexes.html

docs/reference/beds_to_matrix_indexes.html

docs/reference/calculate_CNA.html

docs/reference/calculate_cyto_mat.html

docs/reference/calculate_gain_or_loss.html

docs/reference/calculate_logRatio_CNA.html

docs/reference/call_macs2_merge_peaks.html

docs/reference/changeRange.html

docs/reference/check_correct_datamatrix.html

docs/reference/choose_cluster_scExp-1.png

docs/reference/choose_cluster_scExp-10.png

docs/reference/choose_cluster_scExp-11.png

docs/reference/choose_cluster_scExp-12.png

docs/reference/choose_cluster_scExp-13.png

docs/reference/choose_cluster_scExp-14.png

docs/reference/choose_cluster_scExp-15.png

docs/reference/choose_cluster_scExp-16.png

docs/reference/choose_cluster_scExp-17.png

docs/reference/choose_cluster_scExp-2.png

docs/reference/choose_cluster_scExp-3.png

docs/reference/choose_cluster_scExp-4.png

docs/reference/choose_cluster_scExp-5.png

docs/reference/choose_cluster_scExp-6.png

docs/reference/choose_cluster_scExp-7.png

docs/reference/choose_cluster_scExp-8.png

docs/reference/choose_cluster_scExp-9.png

docs/reference/choose_cluster_scExp.html

docs/reference/choose_perplexity.html

docs/reference/col2hex.html

docs/reference/colors_scExp.html

docs/reference/combine_datamatrix.html

docs/reference/combine_enrichmentTests.html

docs/reference/concatenate_scBed_into_clusters.html

docs/reference/consensus_clustering_scExp-1.png

docs/reference/consensus_clustering_scExp-10.png

docs/reference/consensus_clustering_scExp-11.png

docs/reference/consensus_clustering_scExp-12.png

docs/reference/consensus_clustering_scExp-13.png

docs/reference/consensus_clustering_scExp-14.png

docs/reference/consensus_clustering_scExp-15.png

docs/reference/consensus_clustering_scExp-16.png

docs/reference/consensus_clustering_scExp-17.png

docs/reference/consensus_clustering_scExp-2.png

docs/reference/consensus_clustering_scExp-3.png

docs/reference/consensus_clustering_scExp-4.png

docs/reference/consensus_clustering_scExp-5.png

docs/reference/consensus_clustering_scExp-6.png

docs/reference/consensus_clustering_scExp-7.png

docs/reference/consensus_clustering_scExp-8.png

docs/reference/consensus_clustering_scExp-9.png

docs/reference/consensus_clustering_scExp.html

docs/reference/correlation_and_hierarchical_clust_scExp.html

docs/reference/count_coverage.html

docs/reference/create_project_folder.html

docs/reference/create_sample_name_mat.html

docs/reference/create_scDataset_raw.html

docs/reference/create_scExp.html

docs/reference/define_feature.html

docs/reference/detect_samples.html

docs/reference/differential_analysis_scExp.html

docs/reference/distPearson.html

docs/reference/enrichmentTest.html

docs/reference/exclude_features_scExp.html

docs/reference/feature_annotation_scExp.html

docs/reference/filter_correlated_cell_scExp.html

docs/reference/filter_genes_with_refined_peak_annotation.html

docs/reference/filter_scExp.html

docs/reference/find_top_features.html

docs/reference/gene_set_enrichment_analysis_scExp.html

docs/reference/generate_analysis.html

docs/reference/generate_count_matrix.html

docs/reference/generate_coverage_tracks.html

docs/reference/generate_feature_names.html

docs/reference/getExperimentNames.html

docs/reference/getMainExperiment.html

docs/reference/get_color_dataframe_from_input.html

docs/reference/get_cyto_features.html

docs/reference/get_genomic_coordinates.html

docs/reference/get_most_variable_cyto.html

docs/reference/gg_fill_hue.html

docs/reference/groupMat.html

docs/reference/has_genomic_coordinates.html

docs/reference/hclustAnnotHeatmapPlot.html

docs/reference/hg38.GeneTSS.html

docs/reference/hg38.chromosomes.html

docs/reference/hg38.cytoBand.html

docs/reference/imageCol.html

docs/reference/import_count_input_files.html

docs/reference/import_scExp.html

docs/reference/index.html

docs/reference/index_peaks_barcodes_to_matrix_indexes.html

docs/reference/inter_correlation_scExp.html

docs/reference/intra_correlation_scExp.html

docs/reference/launchApp.html

docs/reference/load_MSIGdb.html

docs/reference/merge_MACS2_peaks.html

docs/reference/mm10.GeneTSS.html

docs/reference/mm10.chromosomes.html

docs/reference/mm10.cytoBand.html

docs/reference/normalize_scExp.html

docs/reference/num_cell_after_QC_filt_scExp.html

docs/reference/num_cell_after_cor_filt_scExp.html

docs/reference/num_cell_before_cor_filt_scExp.html

docs/reference/num_cell_in_cluster_scExp.html

docs/reference/num_cell_scExp.html

docs/reference/pca_irlba_for_sparseMatrix.html

docs/reference/peaks_to_bins.html

docs/reference/plot_cluster_consensus_scExp-1.png

docs/reference/plot_cluster_consensus_scExp.html

docs/reference/plot_coverage_BigWig-1.png

docs/reference/plot_coverage_BigWig.html

docs/reference/plot_differential_H1_scExp-1.png

docs/reference/plot_differential_H1_scExp.html

docs/reference/plot_differential_summary_scExp-1.png

docs/reference/plot_differential_summary_scExp.html

docs/reference/plot_differential_volcano_scExp-1.png

docs/reference/plot_differential_volcano_scExp.html

docs/reference/plot_distribution_scExp-1.png

docs/reference/plot_distribution_scExp.html

docs/reference/plot_gain_or_loss_barplots-1.png

docs/reference/plot_gain_or_loss_barplots-2.png

docs/reference/plot_gain_or_loss_barplots.html

docs/reference/plot_heatmap_scExp-1.png

docs/reference/plot_heatmap_scExp.html

docs/reference/plot_inter_correlation_scExp-1.png

docs/reference/plot_inter_correlation_scExp.html

docs/reference/plot_intra_correlation_scExp-1.png

docs/reference/plot_intra_correlation_scExp.html

docs/reference/plot_most_contributing_features-1.png

docs/reference/plot_most_contributing_features.html

docs/reference/plot_pie_most_contributing_chr-1.png

docs/reference/plot_pie_most_contributing_chr.html

docs/reference/plot_reduced_dim_scExp-1.png

docs/reference/plot_reduced_dim_scExp-2.png

docs/reference/plot_reduced_dim_scExp-3.png

docs/reference/plot_reduced_dim_scExp-4.png

docs/reference/plot_reduced_dim_scExp.html

docs/reference/plot_reduced_dim_scExp_CNA-1.png

docs/reference/plot_reduced_dim_scExp_CNA.html

docs/reference/preprocess_CPM.html

docs/reference/preprocess_RPKM.html

docs/reference/preprocess_TFIDF.html

docs/reference/preprocess_TPM.html

docs/reference/preprocess_feature_size_only.html

docs/reference/raw_counts_to_sparse_matrix.html

docs/reference/rawfile_ToBigWig.html

docs/reference/read_count_mat_with_separated_chr_start_end.html

docs/reference/read_sparse_matrix.html

docs/reference/reduce_dim_batch_correction.html

docs/reference/reduce_dims_scExp.html

docs/reference/remove_chr_M_fun.html

docs/reference/remove_non_canonical_fun.html

docs/reference/results_enrichmentTest.html

docs/reference/retrieve_top_bot_features_pca.html

docs/reference/run_pairwise_tests.html

docs/reference/run_tsne_scExp.html

docs/reference/scExp-1.png

docs/reference/scExp-2.png

docs/reference/scExp-3.png

docs/reference/scExp-4.png

docs/reference/scExp-5.png

docs/reference/scExp.html

docs/reference/separate_BAM_into_clusters.html

docs/reference/separator_count_mat.html

docs/reference/smoothBin.html

docs/reference/subsample_scExp.html

docs/reference/subset_bam_call_peaks.html

docs/reference/swapAltExp_sameColData.html

docs/reference/table_enriched_genes_scExp.html

docs/reference/warning_DA.html

docs/reference/warning_filter_correlated_cell_scExp.html

docs/reference/warning_plot_reduced_dim_scExp.html

docs/reference/warning_raw_counts_to_sparse_matrix.html

docs/reference/wrapper_Signac_FeatureMatrix.html

inst/CITATION

inst/Module_preprocessing_filtering_and_reduction.R

inst/app.js

inst/intro.min.js

inst/js.cookie.js

inst/server.R inst/template.Rmd inst/ui.R

inst/www/ChromSCape_concept.png

inst/www/ChromSCape_logo.png

inst/www/ChromSCape_logo.svg

inst/www/Guide_images/Step1_format_input.png

inst/www/Guide_images/Step1_select_import.png

inst/www/Guide_images/Step2_filter_normalize.png

inst/www/Guide_images/Step3_PCA.png

inst/www/Guide_images/Step3_UMAP.png

inst/www/Guide_images/Step3_contribution_to_PCA.png

inst/www/Guide_images/Step4_1_cluster_cells.png

inst/www/Guide_images/Step4_UMAP.png

inst/www/Guide_images/Step4_intracorrelation.png

inst/www/Guide_images/Step5_peak_calling.png

inst/www/Guide_images/Step6_DA.png

inst/www/Guide_images/Step7_GeneSetAnalysis.png

inst/www/LogoCurie.png

inst/www/app.css

inst/www/app.js

inst/www/intro.min.js

inst/www/introjs.min.css

inst/www/shiny_js_functions.js

inst/www/style.css

longtests/testthat.R longtests/testthat/test_correlation_clustering.R longtests/testthat/test_diff_analysis_gene_set_enrichment.R longtests/testthat/test_processing_filtering.R man/CheA3_TF_nTargets.Rd man/CompareWilcox.Rd man/CompareedgeRGLM.Rd man/DA_custom.Rd man/DA_one_vs_rest.Rd man/DA_pairwise.Rd man/H1proportion.Rd man/annotToCol2.Rd man/annotation_from_merged_peaks.Rd man/anocol_binary.Rd man/anocol_categorical.Rd man/bams_to_matrix_indexes.Rd man/beds_to_matrix_indexes.Rd man/calculate_CNA.Rd man/calculate_cyto_mat.Rd man/calculate_gain_or_loss.Rd man/calculate_logRatio_CNA.Rd man/call_macs2_merge_peaks.Rd man/ce11.GeneTSS.Rd man/ce11.chromosomes.Rd man/changeRange.Rd man/check_correct_datamatrix.Rd man/choose_cluster_scExp.Rd man/choose_perplexity.Rd man/col2hex.Rd man/colors_scExp.Rd man/combine_datamatrix.Rd man/combine_enrichmentTests.Rd man/comparable_variables.Rd man/concatenate_scBed_into_clusters.Rd man/consensus_clustering_scExp.Rd man/correlation_and_hierarchical_clust_scExp.Rd man/count_coverage.Rd man/create_project_folder.Rd man/create_sample_name_mat.Rd man/create_scDataset_raw.Rd man/create_scExp.Rd man/define_feature.Rd man/detect_samples.Rd man/differential_activation.Rd man/differential_analysis_scExp.Rd man/distPearson.Rd man/enrich_TF_ChEA3_genes.Rd man/enrich_TF_ChEA3_scExp.Rd man/enrichmentTest.Rd man/exclude_features_scExp.Rd man/feature_annotation_scExp.Rd man/filter_correlated_cell_scExp.Rd man/filter_genes_with_refined_peak_annotation.Rd man/filter_scExp.Rd man/find_clusters_louvain_scExp.Rd man/find_top_features.Rd man/gene_set_enrichment_analysis_scExp.Rd man/generate_analysis.Rd man/generate_count_matrix.Rd man/generate_coverage_tracks.Rd man/generate_feature_names.Rd man/generate_report.Rd man/getExperimentNames.Rd man/getMainExperiment.Rd man/get_color_dataframe_from_input.Rd man/get_cyto_features.Rd man/get_genomic_coordinates.Rd man/get_most_variable_cyto.Rd man/get_pathway_mat_scExp.Rd man/gg_fill_hue.Rd man/groupMat.Rd man/has_genomic_coordinates.Rd man/hclustAnnotHeatmapPlot.Rd man/hg38.GeneTSS.Rd man/hg38.chromosomes.Rd man/hg38.cytoBand.Rd man/imageCol.Rd man/import_count_input_files.Rd man/import_scExp.Rd man/index_peaks_barcodes_to_matrix_indexes.Rd man/inter_correlation_scExp.Rd man/intra_correlation_scExp.Rd man/launchApp.Rd man/load_MSIGdb.Rd man/merge_MACS2_peaks.Rd man/mm10.GeneTSS.Rd man/mm10.chromosomes.Rd man/mm10.cytoBand.Rd man/normalize_scExp.Rd man/num_cell_after_QC_filt_scExp.Rd man/num_cell_after_cor_filt_scExp.Rd man/num_cell_before_cor_filt_scExp.Rd man/num_cell_in_cluster_scExp.Rd man/num_cell_scExp.Rd man/pca_irlba_for_sparseMatrix.Rd man/plot_cluster_consensus_scExp.Rd man/plot_correlation_PCA_scExp.Rd man/plot_coverage_BigWig.Rd man/plot_differential_summary_scExp.Rd man/plot_differential_volcano_scExp.Rd man/plot_distribution_scExp.Rd man/plot_gain_or_loss_barplots.Rd man/plot_heatmap_scExp.Rd man/plot_inter_correlation_scExp.Rd man/plot_intra_correlation_scExp.Rd man/plot_most_contributing_features.Rd man/plot_percent_active_feature_scExp.Rd man/plot_pie_most_contributing_chr.Rd man/plot_reduced_dim_scExp.Rd man/plot_reduced_dim_scExp_CNA.Rd man/plot_top_TF_scExp.Rd man/plot_violin_feature_scExp.Rd man/preprocess_CPM.Rd man/preprocess_RPKM.Rd man/preprocess_TFIDF.Rd man/preprocess_TPM.Rd man/preprocess_feature_size_only.Rd man/preprocessing_filtering_and_reduction.Rd man/raw_counts_to_sparse_matrix.Rd man/rawfile_ToBigWig.Rd man/read_count_mat_with_separated_chr_start_end.Rd man/read_sparse_matrix.Rd man/rebin_helper.Rd man/rebin_matrix.Rd man/reduce_dim_batch_correction.Rd man/reduce_dims_scExp.Rd man/remove_chr_M_fun.Rd man/remove_non_canonical_fun.Rd man/results_enrichmentTest.Rd man/retrieve_top_bot_features_pca.Rd man/run_pairwise_tests.Rd man/run_tsne_scExp.Rd man/scExp.Rd man/separate_BAM_into_clusters.Rd man/separator_count_mat.Rd man/smoothBin.Rd man/subsample_scExp.Rd man/subset_bam_call_peaks.Rd man/summary_DA.Rd man/swapAltExp_sameColData.Rd man/table_enriched_genes_scExp.Rd man/warning_DA.Rd man/warning_filter_correlated_cell_scExp.Rd man/warning_plot_reduced_dim_scExp.Rd man/warning_raw_counts_to_sparse_matrix.Rd man/wrapper_Signac_FeatureMatrix.Rd

src/RcppExports.cpp

src/as_dist.cpp

tests/testthat.R tests/testthat/test_default_run.R vignettes/vignette.Rmd

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

vallotlab/ChromSCape
Analysis of single-cell epigenomics datasets with a Shiny App

Files in vallotlab/ChromSCape
Analysis of single-cell epigenomics datasets with a Shiny App

R Package Documentation

Browse R Packages

We want your feedback!

vallotlab/ChromSCape Analysis of single-cell epigenomics datasets with a Shiny App

Files in vallotlab/ChromSCape Analysis of single-cell epigenomics datasets with a Shiny App

R Package Documentation

Browse R Packages

We want your feedback!

vallotlab/ChromSCape
Analysis of single-cell epigenomics datasets with a Shiny App

Files in vallotlab/ChromSCape
Analysis of single-cell epigenomics datasets with a Shiny App