Man pages for jokergoo/cotools
R functions

add_subtype_specificityad subtype specificity columns
annotate_to_gene_modelsAnnotate to gene models
annotate_to_genomic_featuressimple annotation to genomic features
available_gencode_fieldReturns all supported fields in gtf data
basic_genomic_regions_statBasic statistics on genomic regions
bpdefine bp
chromatin_states_transition_chord_diagramchord diagram for chromatin states transistion
common_regionsFind common genomic regions across several samples
compare_methcompare methylation between smoothed and raw methylation data
correlated_regionscorrelated regions
correlated_regions_per_genecorrelated regions in extended gene model
cr_enriched_at_tssenrichment of cr on tss
cr_gvizCustomized Gviz plot for a gene model
cr_hilbertHilbert curve visualization of CRs
cr_overlap_to_genomic_featuresenrichment between cr and genomic feature
cr_qcQC on crs
cr_scatterplot_meScatter plot between methylation and expression
enriched_heatmap_list_on_geneEnriched heatmap
enriched_heatmap_list_on_genomic_featuresEnriched heatmap on a certain gf
enriched_heatmap_list_on_tss_cgiEnriched heatmap on TSS-CGI
extract_field_from_gencodeExtract field from gencode GTF file
extract_sitesExtract subset of sites which are in a set of intervals
filter_correlated_regionsfilter correlation regions
genomicCorr.absdistAbsolute distance between two sets of genomic regions
genomicCorr.jaccardJaccard coefficient between two sets of genomic regions
genomicCorr.nintersectIntersections between two sets of genomic regions
genomicCorr.pintersectIntersection between two sets of genomic regions
genomicCorr.reldistRelative distance between two sets of genomic regions
genomicCorr.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 regions
global_methylation_distributionGlobal methylation distribution
heatmap_diff_methylation_in_genomic_featuresHeatmap for mean methylation in genomic features
kbdefine kb
logical_segmentsegment by continuous logical values
mbdefine mb
methylation_hooksHook functions to extract methylation
percentOverlapsFor every interval in 'query', percent that is covered by...
plot_coverage_and_methylation_on_genomecoverage and methylation for one sample
plot_multiple_samples_methylation_on_genomemethylation for more than one samples
plot_subgroup_specificity_heatmapheatmap for visualizing subgroup specific genomic regions
print.bpprint bp class objects
reduce2reduce based on the width of the interval
reduce_crrefuce cr regions
reduce_cr_gap_testplot that helps to choose a gap
scatterplot_with_boxplotscatterplot with boxplots on both sides
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
jokergoo/cotools documentation built on May 18, 2017, 6:05 a.m.