Files in eilslabs/epic
Integrative Analysis and Visualization of Epigenomic Sequencing Data
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/.directory
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/perl_scripts/extract_field_from_gencode.pl
inst/pipeline/.directory
inst/pipeline/pipeline_configure_template.R
inst/pipeline/script/.directory
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
inst/pipeline/test_pipeline/test_pipeline.sh
man/.directory
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
src/RcppExports.cpp
src/RcppExports.o
src/epic.so
src/extract_sites.cpp
src/extract_sites.o
src/rowWhichMax.cpp
src/rowWhichMax.o
tests/test-all.R
tests/testthat/.directory
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
