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SingleMoleculeFootprinting

Analysis tools for Single Molecule Footprinting (SMF) data


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
SingleMoleculeFootprinting HTML R Script
Reference Manual PDF

Details

biocViews Coverage, DNAMethylation, DataRepresentation, Epigenetics, MethylSeq, NucleosomePositioning, QualityControl, Software
Version 1.10.0
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
URL
Bug Reports https://github.com/Krebslabrep/SingleMoleculeFootprinting/issues
See More
Suggests BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0)
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Package Archives

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

Source Package SingleMoleculeFootprinting_1.10.0.tar.gz
Windows Binary SingleMoleculeFootprinting_1.10.0.zip (64-bit only)
macOS Binary (x86_64) SingleMoleculeFootprinting_1.10.0.tgz
macOS Binary (arm64) SingleMoleculeFootprinting_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SingleMoleculeFootprinting
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SingleMoleculeFootprinting
Bioc Package Browser https://code.bioconductor.org/browse/SingleMoleculeFootprinting/
Package Short Url https://bioconductor.org/packages/SingleMoleculeFootprinting/
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