API for jokergoo/epik
Integrative Analysis and Visualization of Epigenomic Sequencing Data

Global functions
[.chromatin_states_transition_matrix Man page
[.subgroup_specific_genomic_regions Man page
add_boxplot_as_column_annotation Source code
add_chord_diagram_legend Source code
add_mean_methylation Source code
add_transparency Source code
annotate_to_gene_models Man page Source code
annotate_to_genomic_features Man page Source code
available_gencode_fields Man page Source code
average_in_window Source code
binary_search Source code
bp Man page Source code
cg_percent_per_window Source code
chipseq_hooks Man page Source code
chromatin_states_transition_chord_diagram Man page Source code
common_regions Man page Source code
compare_meth Man page Source code
constructAnnotationTrack Source code
cor_columns Man page Source code
correlated_regions Man page Source code
correlated_regions_by_window Man page Source code
cr_add_subtype_specificity Man page Source code
cr_concatenate Man page Source code
cr_coverage_on_genes Man page Source code
cr_enriched_heatmap Man page Source code
cr_enriched_heatmap_at_gene Man page Source code
cr_enriched_heatmap_at_genomic_features Man page Source code
cr_enriched_heatmap_at_tss Man page Source code
cr_enriched_heatmap_at_tss_cgi Man page Source code
cr_genes_function_enrichment Source code
cr_genes_gtrellis Man page Source code
cr_genic_stat Man page Source code
cr_gviz Man page Source code
cr_hilbert_curve Man page Source code
cr_reduce Man page Source code
cr_scatterplot Man page Source code
diameter Source code
dist_by_closeness Source code
dist_by_closeness2 Source code
do_david Source code
enrich_with_histone_mark Man page Source code
enrich_with_methylation Man page Source code
extract_field_from_gencode Man page Source code
extract_sites Man page Source code
find_neighbours Man page Source code
format_sample_id_and_subgroup Source code
general_chipseq_association Man page Source code
general_chipseq_association_to_methylation Man page Source code
generate_background_from_methylation_features Source code
generate_color_fun Source code
generate_diff_color_fun Source code
genomic_corr_absdist Man page Source code
genomic_corr_intersect Man page Source code
genomic_corr_jaccard Man page Source code
genomic_corr_reldist Man page Source code
genomic_regions_basic_stat Man page Source code
genomic_regions_correlation Man page Source code
getChromInfoFromUCSC Source code
get_chipseq_association_stat Source code
get_chromHMM_list Man page Source code
get_mean_methylation_in_genomic_features Man page Source code
get_peak_list Man page Source code
get_sig_cr Man page Source code
gp_c Source code
heatmap_diff_methylation_in_genomic_features Man page Source code
heatmap_subgroup_specificity Man page Source code
hilbert_curve_chipseq_difference Man page Source code
hilbert_curve_methylation_difference Man page Source code
import_gencode_as_txdb Man page Source code
initialize_project_directory Man page Source code
is.file Source code
is.not.null Source code
kb Man page Source code
load_epik_config Man page Source code
make_ecdf Source code
make_transition_matrix_from_chromHMM Man page Source code
make_upset Source code
mat_dist Man page Source code
match_by_gencode Man page Source code
max_reduce_of_significance Source code
mb Man page Source code
mean_chromHMM_overlap Source code
mean_overlap Source code
merge_cpg_dinucleotide_methylation Man page Source code
merge_row_order Source code
methylation_global_distribution Man page Source code
methylation_gtrellis Man page Source code
methylation_gtrellis_multiple_samples Man page Source code
methylation_hooks Man page Source code
methylation_qcplot Man page Source code
normalize_epigenomic_signals Source code
percentOverlaps Man page Source code
plot_upset Source code
print.bp Man page Source code
print.chromatin_states_transition_matrix Man page Source code
print.methylation_hooks Man page Source code
print.subgroup_specific_genomic_regions Man page Source code
pushTrackList Source code
qq_message Source code
qq_stop Source code
qq_warning Source code
read.chromInfo Source code
readRDS_or_readRData Source code
reduce2 Man page Source code
reduce_cr_by_gene Source code
reduce_david_results Man page Source code
register_global_var Man page Source code
return2 Source code
rowWhichMax Source code
scatterplot_with_boxplot Man page Source code
set_chr Source code
set_counter Man page Source code
set_proper_seqlengths Source code
sig_cr_compare_cutoff Man page Source code
sig_cr_enriched_heatmap Man page Source code
sig_cr_heatmap Man page Source code
sig_cytoband_gtrellis Man page Source code
state_names Man page Source code
state_names<- Man page
strwrap2 Source code
subgroup_specific_genomic_regions Man page Source code
submit_to_david Man page Source code
systemdf Man page Source code
t.chromatin_states_transition_matrix Man page Source code
weighted_mean Source code
jokergoo/epik documentation built on Feb. 14, 2018, 2:24 p.m.