Files in eilslabs/epic

Integrative Analysis and Visualization of Epigenomic Sequencing Data

R/RcppExports.R R/Rcpp_interface.R R/chromatin_states_transitions.R R/common_utils.R R/epic.R R/extract_site.R R/function_memorized.R R/gencode_utils.R R/genomic_region_annotation.R R/genomic_region_correlation.R R/genomic_region_merge.R R/genomic_region_stat.R R/genomic_region_subgroup_specificity.R R/hooks.R R/load_config.R R/methylation_cr.R R/methylation_cr_downstream.R R/methylation_cr_enriched.R R/methylation_cr_gviz.R R/methylation_cr_scatterplot.R R/methylation_genomic_features.R R/methylation_stat.R R/methylation_subtype_classification.R R/pipeline.R R/systemdf.R README.md inst/pipeline/pipeline_configure_template.R inst/pipeline/script/chromatin_states_transitions.R inst/pipeline/script/correlated_regions.R inst/pipeline/script/correlated_regions_downstream.R inst/pipeline/script/correlated_regions_enriched.R inst/pipeline/script/correlated_regions_filter.R inst/pipeline/script/correlated_regions_gviz.R inst/pipeline/script/correlated_regions_reduce.R inst/pipeline/script/differential_methylation_in_cgi_and_shore.R inst/pipeline/script/differential_methylation_in_genomic_features.R inst/pipeline/script/general_methylation_distribution.R inst/pipeline/script/methylation_subtype_classification_in_cgi_and_shore.R inst/pipeline/test_pipeline/roadmap_configure.R man/annotate_to_gene_models.rd man/annotate_to_genomic_features.rd man/available_gencode_fields.rd man/basic_genomic_regions_stat.rd man/binary_search.rd man/bp.rd man/chipseq_hooks.rd man/chromatin_states_transition_chord_diagram.rd man/common_regions.rd man/cor_columns.rd man/correlated_regions.rd man/cr_add_subtype_specificity.rd man/cr_enriched_at_tss.rd man/cr_gviz.rd man/cr_hilbert.rd man/cr_overlap_to_genomic_features.rd man/cr_scatterplot_me.rd man/enriched_heatmap_list_on_gene.rd man/enriched_heatmap_list_on_genomic_features.rd man/enriched_heatmap_list_on_tss_cgi.rd man/epic.rd man/extract_field_from_gencode.rd man/extract_sites.rd man/filter_correlated_regions.rd man/find_neighbours.rd man/genomic_corr_absdist.rd man/genomic_corr_jaccard.rd man/genomic_corr_nintersect.rd man/genomic_corr_pintersect.rd man/genomic_corr_reldist.rd man/genomic_corr_sintersect.rd man/genomic_regions_correlation.rd man/get_mean_methylation_in_genomic_features.rd man/get_peak_list.rd man/global_methylation_distribution.rd man/heatmap_diff_methylation_in_genomic_features.rd man/kb.rd man/load_config.rd man/logical_segment.rd man/make_transition_matrix_from_chromHMM.rd man/mb.rd man/methylation_hooks.rd man/methylation_subtype_classfication.rd man/percentOverlaps.rd man/plot_coverage_and_methylation_on_genome.rd man/plot_multiple_samples_methylation_on_genome.rd man/plot_subgroup_specificity_heatmap.rd man/print.bp.rd man/reduce2.rd man/reduce_cr.rd man/reduce_cr_gap_test.rd man/run_pipeline.rd man/scatterplot_with_boxplot.rd man/set_counter.rd man/subgroup_specific_genomic_regions.rd man/systemdf.rd man/wgbs_qcplot.rd tests/test-all.R tests/testthat/test_chord_diagram.R tests/testthat/test_extract_sites.R tests/testthat/test_find_neighbours.R tests/testthat/test_genomic_annotation.R tests/testthat/test_genomic_regions_correlation.R tests/testthat/test_genomic_regions_ss.R tests/testthat/test_logical_segment.R tests/testthat/test_methylation_stat.R tests/testthat/test_reduce2.R tests/testthat/test_systemdf.R