SingleMoleculeFootprinting

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see SingleMoleculeFootprinting.

Analysis tools for Single Molecule Footprinting (SMF) data

DOI: 10.18129/B9.bioc.SingleMoleculeFootprinting

Bioconductor version: 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 iD ORCID: 0000-0001-6066-3920 , Arnaud Krebs [aut] ORCID iD ORCID: 0000-0001-7999-6127 , Mike Smith [ctb] ORCID iD ORCID: 0000-0002-7800-3848

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")
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")

FootprintCharter.html HTML R Script

methylation_calling_and_QCs.html HTML R Script

single_molecule_sorting_by_TF.html HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DNAMethylation, DataRepresentation, Epigenetics, MethylSeq, NucleosomePositioning, QualityControl, Sequencing, Software

Version 2.2.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 years)

License GPL-3

Depends R (>= 4.4.0)

Imports BiocGenerics, Biostrings, BSgenome, cluster, dplyr, GenomeInfoDb, GenomicRanges, ggpointdensity, ggplot2, ggrepel, grDevices, IRanges, magrittr, Matrix, methods, miscTools, parallel, parallelDist, patchwork, plyranges, QuasR, RColorBrewer, rlang, S4Vectors, stats, stringr, tibble, tidyr, utils, viridis

System Requirements

URL https://www.bioconductor.org/packages/release/bioc/html/SingleMoleculeFootprinting.html

Bug Reports https://github.com/Krebslabrep/SingleMoleculeFootprinting/issues

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

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Package Archives

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

Source Package SingleMoleculeFootprinting_2.2.0.tar.gz

Windows Binary (x86_64) SingleMoleculeFootprinting_2.2.0.zip (64-bit only)

macOS Binary (x86_64) SingleMoleculeFootprinting_2.2.0.tgz

macOS Binary (arm64) SingleMoleculeFootprinting_2.2.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/SingleMoleculeFootprinting

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SingleMoleculeFootprinting

Bioc Package Browser https://code.bioconductor.org/browse/SingleMoleculeFootprinting/

Package Short Url https://bioconductor.org/packages/SingleMoleculeFootprinting/

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