Man pages for eilslabs/epic
Integrative Analysis and Visualization of Epigenomic Sequencing Data

annotate_to_gene_modelsAnnotate to gene models
annotate_to_genomic_featuresAnnotate to genomic features
available_gencode_fieldsReturns all supported fields in GTF data
basic_genomic_regions_statBasic statistics on genomic regions
binary_searchFind intervals by binary search
bpMark the numbers to be number of base pairs
chipseq_hooksHook functions to extract ChIP-Seq peak data
chromatin_states_transition_chord_diagramChord diagram for chromatin states transistion
common_regionsFind common genomic regions across several samples
cor_columnsNumber of columns which are highly correlated to other...
correlated_regionsCorrelation between methylation and expression
cr_add_subtype_specificityAdd subtype specificity columns in cr
cr_enriched_at_tssEnrichment of cr around tss
cr_gvizCustomized Gviz plot for a gene model
cr_hilbertHilbert curve visualization of correlated regions
cr_overlap_to_genomic_featuresEnrichment of cr to other genomic features
cr_scatterplot_meScatter plot between methylation and expression in a...
enriched_heatmap_list_on_geneEnriched heatmaps to visualize how signals are enriched at...
enriched_heatmap_list_on_genomic_featuresEnriched heatmaps to visualize how signals are enriched at a...
enriched_heatmap_list_on_tss_cgiEnriched heatmaps to visualize how signals are at enriched...
epicRun pre-defiend scripts
extract_field_from_gencodeExtract field from gencode GTF file
extract_sitesExtract subset of sites in a set of intervals
filter_correlated_regionsGet correlated regions with significant correlations
find_neighboursFind neighbour regions
genomic_corr_absdistAbsolute distance between two sets of genomic regions
genomic_corr_jaccardJaccard coefficient between two sets of genomic regions
genomic_corr_nintersectIntersections between two sets of genomic regions
genomic_corr_pintersectIntersection between two sets of genomic regions
genomic_corr_reldistRelative distance between two sets of genomic regions
genomic_corr_sintersectIntersection between two sets of genomic regions
genomic_regions_correlationCorrelation between two sets of genomic regions
get_mean_methylation_in_genomic_featuresCalculate mean methylation value in a list of genomic...
get_peak_listGet a list of peak regions
global_methylation_distributionGlobal methylation distribution
heatmap_diff_methylation_in_genomic_featuresHeatmap for differential methylation in genomic features
kbMark that the numbers represent number of kilo bases
load_configLoad and validate configuration file
logical_segmentSegmentation by a logical vector
make_transition_matrix_from_chromHMMGenerate transition matrix from chromHMM results
mbMark that the numbers represent number of mega bases
methylation_hooksHook functions to extract methylation data
methylation_subtype_classficationClassify subtypes by methylation data
percentOverlapsFind overlapping genomic regions
plot_coverage_and_methylation_on_genomePlot coverage and methylation for a single sample
plot_multiple_samples_methylation_on_genomePlot methylation for multiple samples
plot_subgroup_specificity_heatmapHeatmap for visualizing subgroup specific genomic regions
print.bpPrint bp class objects
reduce2Merge genomic regions
reduce_crMerge neighbouring cr regions
reduce_cr_gap_testTest a proper gap value for cr merging
run_pipelinerun pipeline through qsub system
scatterplot_with_boxplotScatterplot with boxplots on both sides
set_counterSet a counter which represents percent finished in a loop
subgroup_specific_genomic_regionsFind subgroup specific regions
systemdfWrapper of system calls in which input and output are all...
wgbs_qcplotBasic qc plot for bisulfite sequencing data
eilslabs/epic documentation built on May 13, 2017, 3:07 p.m.