Files in jokergoo/epik

Integrative Analysis and Visualization of Epigenomic Sequencing Data

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

NEWS

R/.directory

R/Rcpp_interface.R R/cache.R R/chromatin_states_transitions.R R/code_snippet.R R/common_utils.R R/compare_meth.R R/correlated_regions.R R/correlated_regions_enrich.R R/correlated_regions_enrichedheatmap.R R/correlated_regions_gene_functions.R R/correlated_regions_genic_stat.R R/correlated_regions_global_vis.R R/correlated_regions_gviz.R R/correlated_regions_scatterplot.R R/correlated_regions_sig_heatmap.R R/cpg_dinucleotide_methylation.R R/david_dws.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/hilbert_curve_difference.R R/import_gencode.R R/load_epik_config.R R/methylation_feature_enrichment.R R/methylation_genomic_features.R R/methylation_qc_and_distribution.R R/read_data_hooks.R R/systemdf.R R/upset.R README.md

inst/chrom_info_list.rds

inst/perl_scripts/extract_field_from_gencode.pl

load.R

man/.directory

man/Extract.chromatin_states_transition_matrix.rd man/Extract.subgroup_specific_genomic_regions.rd man/annotate_to_gene_models.rd man/annotate_to_genomic_features.rd man/available_gencode_fields.rd man/bp.rd man/chipseq_hooks.rd man/chromatin_states_transition_chord_diagram.rd man/common_regions.rd man/compare_meth.rd man/cor_columns.rd man/correlated_regions.rd man/correlated_regions_by_window.rd man/cr_add_subtype_specificity.rd man/cr_concatenate.rd man/cr_coverage_on_genes.rd man/cr_enriched_heatmap.rd man/cr_enriched_heatmap_at_gene.rd man/cr_enriched_heatmap_at_genomic_features.rd man/cr_enriched_heatmap_at_tss.rd man/cr_enriched_heatmap_at_tss_cgi.rd man/cr_genes_gtrellis.rd man/cr_genic_stat.rd man/cr_gviz.rd man/cr_hilbert_curve.rd man/cr_reduce.rd man/cr_scatterplot.rd man/enrich_with_histone_mark.rd man/enrich_with_methylation.rd man/extract_field_from_gencode.rd man/extract_sites.rd man/find_neighbours.rd man/general_chipseq_association.rd man/general_chipseq_association_to_methylation.rd man/genomic_corr_absdist.rd man/genomic_corr_intersect.rd man/genomic_corr_jaccard.rd man/genomic_corr_reldist.rd man/genomic_regions_basic_stat.rd man/genomic_regions_correlation.rd man/get_chromHMM_list.rd man/get_mean_methylation_in_genomic_features.rd man/get_peak_list.rd man/get_sig_cr.rd man/heatmap_diff_methylation_in_genomic_features.rd man/heatmap_subgroup_specificity.rd man/hilbert_curve_chipseq_difference.rd man/hilbert_curve_methylation_difference.rd man/import_gencode_as_txdb.rd man/initialize_project_directory.rd man/kb.rd man/load_epik_config.rd man/make_transition_matrix_from_chromHMM.rd man/mat_dist.rd man/match_by_gencode.rd man/mb.rd man/merge_cpg_dinucleotide_methylation.rd man/methylation_global_distribution.rd man/methylation_gtrellis.rd man/methylation_gtrellis_multiple_samples.rd man/methylation_hooks.rd man/methylation_qcplot.rd man/percentOverlaps.rd man/print.bp.rd man/print.chromatin_states_transition_matrix.rd man/print.methylation_hooks.rd man/print.subgroup_specific_genomic_regions.rd man/reduce2.rd man/reduce_david_results.rd man/register_global_var.rd man/scatterplot_with_boxplot.rd man/set_counter.rd man/sig_cr_compare_cutoff.rd man/sig_cr_enriched_heatmap.rd man/sig_cr_heatmap.rd man/sig_cytoband_gtrellis.rd man/state_names.rd man/state_namesAssign.rd man/subgroup_specific_genomic_regions.rd man/submit_to_david.rd man/systemdf.rd man/t.chromatin_states_transition_matrix.rd roadmap/00.generate_meth_dataset.R roadmap/00.generate_txdb.R roadmap/00.sample_coverage_NA_rate.R roadmap/00.sample_subgroup.R roadmap/cr.R roadmap/data_config.R roadmap/docs/01.import_data.Rmd

roadmap/docs/01.import_data.html

roadmap/docs/01.import_data.md roadmap/docs/02.genomic_regions_utilities.Rmd

roadmap/docs/02.genomic_regions_utilities.html

roadmap/docs/02.genomic_regions_utilities.md roadmap/docs/03.methylation_utilities.Rmd

roadmap/docs/03.methylation_utilities.html

roadmap/docs/03.methylation_utilities.md roadmap/docs/04.hilbert_curve_diff.Rmd

roadmap/docs/04.hilbert_curve_diff.html

roadmap/docs/04.hilbert_curve_diff.md

roadmap/figure/basic_genomic_regions_stat-1.png

roadmap/figure/basic_genomic_regions_stat-2.png

roadmap/figure/basic_genomic_regions_stat-3.png

roadmap/figure/basic_genomic_regions_stat-4.png

roadmap/figure/genomic_regions_correlation-1.png

roadmap/figure/global_methylation_distribution-1.png

roadmap/figure/global_methylation_distribution-2.png

roadmap/figure/global_methylation_distribution-3.png

roadmap/figure/global_methylation_distribution-4.png

roadmap/figure/global_methylation_distribution-5.png

roadmap/figure/global_methylation_distribution-6.png

roadmap/figure/gtrellis_coverage_and_methylation-1.png

roadmap/figure/gtrellis_methylation_for_multiple_samples-1.png

roadmap/figure/heatmap_diff_methylation_in_genomic_features-1.png

roadmap/figure/subgroup_specific_genomic_regions-1.png

roadmap/figure/unnamed-chunk-3-1.png

roadmap/figure/unnamed-chunk-3-2.png

roadmap/figure/unnamed-chunk-3-3.png

roadmap/figure/unnamed-chunk-3-4.png

roadmap/figure/unnamed-chunk-4-1.png

roadmap/figure/unnamed-chunk-4-2.png

roadmap/figure/unnamed-chunk-4-3.png

roadmap/figure/unnamed-chunk-4-4.png

roadmap/figure/unnamed-chunk-4-5.png

roadmap/figure/unnamed-chunk-4-6.png

roadmap/figure/unnamed-chunk-4-7.png

roadmap/figure/unnamed-chunk-5-1.png

roadmap/figure/unnamed-chunk-6-1.png

roadmap/figure/unnamed-chunk-6-10.png

roadmap/figure/unnamed-chunk-6-2.png

roadmap/figure/unnamed-chunk-6-3.png

roadmap/figure/unnamed-chunk-6-4.png

roadmap/figure/unnamed-chunk-6-5.png

roadmap/figure/unnamed-chunk-6-6.png

roadmap/figure/unnamed-chunk-6-7.png

roadmap/figure/unnamed-chunk-6-8.png

roadmap/figure/unnamed-chunk-6-9.png

roadmap/figure/wgbs_qcplot-1.png

roadmap/figure/wgbs_qcplot-2.png

roadmap/figure/wgbs_qcplot-3.png

roadmap/merge_cr.R

roadmap/scripts/.directory

roadmap/scripts/00.generate_txdb.R roadmap/scripts/00.make_rds_for_methylation_data.R roadmap/scripts/00.sample_coverage_NA_rate.R roadmap/scripts/01.global_methylation_distribution.R roadmap/scripts/01.hilbert_curve_global_difference.R roadmap/scripts/01.sample_groups.R roadmap/scripts/02.correlated_regions.R roadmap/scripts/02.correlated_regions_concatenate.R roadmap/scripts/02.correlated_regions_reduce.R roadmap/scripts/03.compare_smooth.R roadmap/scripts/03.correlated_regions_general_correlation.R roadmap/scripts/03.correlated_regions_misc.R roadmap/scripts/03.correlated_regions_sig_heatmap.R roadmap/scripts/04.correlated_regions_enrichedheatmap_at_cgi.R roadmap/scripts/04.correlated_regions_enrichedheatmap_at_gene.R roadmap/scripts/04.correlated_regions_enrichedheatmap_at_genomicfeatures.R roadmap/scripts/04.correlated_regions_genic_stat.R roadmap/scripts/04.correlated_regions_gviz.R roadmap/scripts/05.chromatin_states.R roadmap/scripts/configure/roadmap_configure.R roadmap/scripts/configure/roadmap_configure_primary.R roadmap/scripts/lib/chromatin_states_transitions.R

roadmap/scripts/lib/dist_by_closeness.cpp

roadmap/scripts/lib/extract_sites.cpp

roadmap/scripts/lib/hooks.R roadmap/scripts/lib/methylation_cr.R roadmap/scripts/lib/methylation_cr_enriched.R roadmap/scripts/lib/methylation_cr_gviz.R roadmap/scripts/lib/methylation_cr_hc.R roadmap/scripts/lib/methylation_cr_scatterplot.R roadmap/scripts/lib/methylation_distribution.R roadmap/scripts/lib/utils.R

roadmap/scripts/perl/extract_field_from_gencode.pl

roadmap/scripts/readme.md

roadmap/scripts/unused/00.filter_protein_coding.sh

roadmap/scripts/unused/04.correlated_regions_enrichedheatmap_at_gene_original.R roadmap/scripts/unused/compare_gencode.R roadmap/scripts/unused/correlated_regions_cr_compare.R roadmap/scripts/unused/correlated_regions_downstream_bk.R roadmap/scripts/unused/correlated_regions_enriched.R roadmap/scripts/unused/correlated_regions_filter.R roadmap/scripts/unused/correlated_regions_general_correlation_bk.R roadmap/scripts/unused/correlated_regions_general_heatmap.R roadmap/scripts/unused/sample_groups_bk.R

roadmap/submit.sh

src/RcppExports.cpp

src/RcppExports.o

src/dist_by_closeness.cpp

src/dist_by_closeness.o

src/epik.so

src/extract_sites.cpp

src/extract_sites.o

src/rowWhichMax.cpp

src/rowWhichMax.o

tests_not_run/test_chromatin_states_transition.R tests_not_run/test_correlated_regions.R tests_not_run/test_cpg_dinucleotide_methylation.R tests_not_run/test_cr_enrichedheatmap.R tests_not_run/test_cr_genic_stat.R tests_not_run/test_cr_global_vis.R tests_not_run/test_cr_gviz.R tests_not_run/test_cr_head.R tests_not_run/test_cr_scatterplot.R tests_not_run/test_cr_sig_heatmap.R tests_not_run/test_genomic_regions_annotation.R tests_not_run/test_genomic_regions_correlation.R tests_not_run/test_genomic_regions_merge.R tests_not_run/test_genomic_regions_ss.R tests_not_run/test_genomic_regions_stat.R tests_not_run/test_hc_difference.R tests_not_run/test_head.R tests_not_run/test_import_gencode.R tests_not_run/test_io_hooks.R tests_not_run/test_methylation_gf.R tests_not_run/test_methylation_qc_and_global_dist.R tests_not_run/test_systemdf.R

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.