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

annotate_to_gene_modelsAnnotate genomic regions to gene models
annotate_to_genomic_featuresAnnotate genomic regions to a list of genomic features
available_gencode_fieldsReturns all supported fields in GTF file
bpAdd unit "bp" to the number
chipseq_hooksRead ChIP-Seq dataset
chromatin_states_transition_chord_diagramChord diagram for visualizing chromatin states transitions
common_regionsFind common genomic regions across samples
compare_methCompare raw and smoothed methylation
cor_columnsNumber of columns which are highly correlated to other...
correlated_regionsCorrelation between methylation and expression
correlated_regions_by_windowCorrelated regions in a specified region
cr_add_subtype_specificityAdd subtype specificity columns in CR
cr_concatenateConcatenate CR objects
cr_coverage_on_genesCR coverage on genes
cr_enriched_heatmapVisualize landscape of genome-wide correlations
cr_enriched_heatmap_at_geneVisualizing enrichment for epigenomic signals at gene body
cr_enriched_heatmap_at_genomic_featuresVisualizing enrichment for epigenomic signals at TSS-CGIs
cr_enriched_heatmap_at_tssVisualizing enrichment for epigenomic signals at TSS
cr_enriched_heatmap_at_tss_cgiVisualizing enrichment for epigenomic signals at TSS-CGIs
cr_genes_gtrellisVisualize CR genes in gtrellis layout
cr_genic_statPlot general statistics for the annotations to genes
cr_gvizCustomized Gviz plot for a single gene
cr_hilbert_curveVisualize global correlation by Hilbert curve
cr_reduceMerge correlated regions
cr_scatterplotScatter plot between methylation and expression in one...
enrich_with_histone_markNormalize histone modification signals to target regions
enrich_with_methylationNormalize methylation to target regions
Extract.chromatin_states_transition_matrixSubset chromatin_states_transition_matrix class object
extract_field_from_gencodeExtract field from gencode GTF file
extract_sitesExtract subset of sites in a set of intervals
Extract.subgroup_specific_genomic_regionsSubset the subgroup_specific_genomic_regions class object
find_neighboursFind neighbour regions
general_chipseq_associationGeneral association between histone modifications
general_chipseq_association_to_methylationGeneral association between histone modifications and...
genomic_corr_absdistAbsolute distance between two sets of genomic regions
genomic_corr_intersectIntersections between two sets of genomic regions
genomic_corr_jaccardJaccard coefficient between two sets of genomic regions
genomic_corr_reldistRelative distance between two sets of genomic regions
genomic_regions_basic_statVisualize basic statistics on genomic regions
genomic_regions_correlationCorrelation between two sets of genomic regions
get_chromHMM_listGet a list of chromatin segmentation regions
get_mean_methylation_in_genomic_featuresCalculate mean methylation in a list of genomic features
get_peak_listGet a list of peak regions for a given histone mark
get_sig_crGet significant CRs
heatmap_diff_methylation_in_genomic_featuresHeatmap for differential methylated genomic features
heatmap_subgroup_specificityHeatmap for visualizing subgroup specific genomic regions
hilbert_curve_chipseq_differenceVisualize ChIP-Seq signal difference by Hilbert curve
hilbert_curve_methylation_differenceVisualize methylation difference by Hilbert curve
import_gencode_as_txdbImport gencode GTF file as a TxDb object
initialize_project_directoryInitialize project directories
kbAdd unit "kb" to the number
load_epik_configLoad and validate configuration file
make_transition_matrix_from_chromHMMGenerate transition matrix from chromHMM results
match_by_gencodeFilter one GTF annotation by another
mat_distVisualize distribution of a matrix or a list
mbAdd unit "mb" to the number
merge_cpg_dinucleotide_methylationMerge methylation for CpG dinucleotide
methylation_global_distributionGlobal methylation distribution
methylation_gtrellisPlot coverage and methylation for a single sample
methylation_gtrellis_multiple_samplesPlot methylation for multiple samples as heatmaps
methylation_hooksRead methylation dataset
methylation_qcplotBasic qc plot for distribution of methylation and CpG...
percentOverlapsOverlap genomic regions
print.bpPrint the bp object
print.chromatin_states_transition_matrixPrint chromatin_states_transition_matrix class object
print.methylation_hooksPrint the methylation_hooks object
print.subgroup_specific_genomic_regionsPrint subgroup_specific_genomic_regions class object
reduce2Merge genomic regions
reduce_david_resultsreduce david results
register_global_varRegister global variables
scatterplot_with_boxplotScatterplot with boxplots on both sides
set_counterSet a counter which represents the percentage finished in a...
sig_cr_compare_cutoffCompare cutoff for determining significant correlated regions
sig_cr_enriched_heatmapVisualize significantly correlated regions
sig_cr_heatmapHeatmaps for significant correlated regions
sig_cytoband_gtrellisVisualize correlations in cytoband
state_namesSimply return names of chromatin states
state_namesAssignChange chromatin state names
subgroup_specific_genomic_regionsFind subgroup specific regions
submit_to_davidDoing DAVID analysis
systemdfWrapper of system calls in which input and output are all...
t.chromatin_states_transition_matrixTranspose the chromatin transition matrix
jokergoo/epik documentation built on Feb. 14, 2018, 2:24 p.m.