SingleMoleculeFootprinting

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 (3.21)

SingleMoleculeFootprinting provides 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] (ORCID: ), Arnaud Krebs [aut] (ORCID: ), Mike Smith [ctb] (ORCID: )

Maintainer: Guido Barzaghi <guido.barzaghi at embl.de>

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SingleMoleculeFootprinting")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DNAMethylation, DataRepresentation, Epigenetics, MethylSeq, NucleosomePositioning, QualityControl, Sequencing, Software
Version	2.1.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 years)
License	GPL-3
Depends	R (>= 4.4.1)
Imports	BiocGenerics, Biostrings, BSgenome, dplyr, GenomeInfoDb, GenomicRanges, ggpointdensity, ggplot2, ggrepel, grDevices, IRanges, Matrix, parallel, patchwork, plyr, plyranges, QuasR, RColorBrewer, rlang, S4Vectors, stats, stringr, tibble, tidyr, tidyverse, viridis
System Requirements
URL
Bug Reports	https://github.com/Krebslabrep/SingleMoleculeFootprinting/issues

Suggests	BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, qs, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0)
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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