Tools

Import Pycallingcards as:

import pycallingcards as cc

tools.call_motif	Call motif by HOMER and [Heinz et al., 2010].
tools.compare_motif	Compare the motifs from the motif results of two groups from HOMER and [Heinz et al., 2010].
tools.rank_peak_groups	Rank peaks for characterizing groups.
tools.rank_peak_groups_mu	Rank peaks for characterizing groups.
tools.rank_peak_groups_df	pycallingcards.tl.rank_peak_groups() results in the form of a DataFrame.
tools.diff2group_bygroup	Compare the peak difference between two groups for specific peak by group.
tools.diff2group_bysample	Comapare the peak difference between two groups for a specific peak by sample.
tools.DE_pvalue	Compare the peak difference between two groups for specific peak.
tools.pair_peak_gene_bulk	Pair related peaks and genes.
tools.pair_peak_gene_sc	Pair related peaks and genes.
tools.pair_peak_gene_sc_mu	Pair related peaks and genes.
tools.liftover	Use liftover to transform from one genome to another [Hinrichs et al., 2006].
tools.find_location	Find the gene location for a specfic genome.
tools.result_mapping	Map from one genome to another for the result table [Hinrichs et al., 2006].
tools.GWAS	Calculate the GWAS result for the peak in the data.
tools.GWAS_adata_bulk	Plot GWAS results for different cell types for bulk calling cards data.
tools.GWAS_adata_sc	Plot GWAS results for different cell types for single-cell calling cards data.
tools.footprint	Find the CC footprint in yeast CC data.
tools.find_fastq	Find the fastq file of a specific part of a gene.