In CompEpigen/scMethrix: Fast and efficient summarization of single cell whole genome bisulfate data

Integration with other tools

scMethrix has multiple options to export data for different purposes. The write_bedgraph function supports a bedgraph format, that can be directly uploaded to UCSC. The multibed option generates a file with all samples as columns. The metilene option ensures that this file is in the correct format for metilene, a command line DMR caller.

# UCSC browser
export_bedgraphs(m = meth, output_dir = ".")
# Metilene
write_bedgraphs(m = meth, output_dir = ".", rm_NA = FALSE, metilene = TRUE,multiBed = "metline_ip", phenoCol = "Day")

We also support bigWig format.

write_bigwigs(meth, output_dir = ".", samp_names = NULL)

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.