Registration Open for Bioc2024 July 24-26


This is the development version of SingleMoleculeFootprinting; for the stable release version, see SingleMoleculeFootprinting.

Analysis tools for Single Molecule Footprinting (SMF) data

Bioconductor version: Development (3.20)

SingleMoleculeFootprinting is an R package providing functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location

Author: Guido Barzaghi [aut, cre] , Arnaud Krebs [aut] , Mike Smith [ctb]

Maintainer: Guido Barzaghi <guido.barzaghi at>

Citation (from within R, enter citation("SingleMoleculeFootprinting")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

SingleMoleculeFootprinting HTML R Script
Reference Manual PDF


biocViews Coverage, DNAMethylation, DataRepresentation, Epigenetics, MethylSeq, NucleosomePositioning, QualityControl, Software
Version 1.13.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 4.1.0)
Imports BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicRanges, data.table, grDevices, plyr, IRanges, RColorBrewer, stats, QuasR
System Requirements
Bug Reports
See More
Suggests BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0)
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SingleMoleculeFootprinting_1.13.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) SingleMoleculeFootprinting_1.13.0.tgz
macOS Binary (arm64) SingleMoleculeFootprinting_1.13.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats