footprintR provides tools for working with single-molecule footprinting data
in R. These include functions for reading base modifications from bam files or
files generated by modkit, efficient
representation of such data as R objects, and functions to manipulate and
visualize such objects.
Current contributors include:
footprintR can be installed from GitHub via the
BiocManager package:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("fmicompbio/footprintR")
Here is a minimal example to for using footprintR:
library(footprintR)
infile <- system.file("extdata", "modkit_pileup_1.bed.gz", package = "footprintR")
se <- readBedMethyl(bmfile, modbase = "m")
se
assayNames(se)
The return value se is a SummarizedExperiment with positions in rows and
samples in columns, and assays Nmod and Nvalid with the counts of modified
and total (valid) bases.
The results can be conveniently visualized:
plotRegion(se)
Github Actions (multiple OS): 
