SingleMoleculeFootprinting

DOI: 10.18129/B9.bioc.SingleMoleculeFootprinting    

Analysis tools for Single Molecule Footprinting (SMF) data

Bioconductor version: Release (3.14)

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 embl.de>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SingleMoleculeFootprinting")

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

Documentation

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

browseVignettes("SingleMoleculeFootprinting")

 

HTML	R Script	SingleMoleculeFootprinting
PDF		Reference Manual

Details

biocViews	Coverage, DNAMethylation, DataRepresentation, Epigenetics, MethylSeq, NucleosomePositioning, QualityControl, Software
Version	1.2.0
In Bioconductor since	BioC 3.13 (R-4.1) (1 year)
License	GPL-3
Depends	R (>= 4.1.0)
Imports	BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicRanges, data.table, grDevices, plyr, IRanges, RColorBrewer, stats, QuasR
LinkingTo
Suggests	BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL
BugReports	https://github.com/Krebslabrep/SingleMoleculeFootprinting/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SingleMoleculeFootprinting_1.2.0.tar.gz
Windows Binary	SingleMoleculeFootprinting_1.2.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	SingleMoleculeFootprinting_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SingleMoleculeFootprinting
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SingleMoleculeFootprinting
Package Short Url	https://bioconductor.org/packages/SingleMoleculeFootprinting/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive