Files in vallotlab/ChromSCape

Analysis of single-cell epigenomics datasets with a Shiny App

.BBSoptions

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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

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inst/CITATION

inst/Module_preprocessing_filtering_and_reduction.R

inst/app.js

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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.