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Bioconductor - SingleMoleculeFootprinting

SingleMoleculeFootprinting

This is the released version of SingleMoleculeFootprinting; for the devel version, see SingleMoleculeFootprinting.

Analysis tools for Single Molecule Footprinting (SMF) data

Bioconductor version: Release (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: 0000-0001-6066-3920 , Arnaud Krebs [aut] ORCID: 0000-0001-7999-6127 , Mike Smith [ctb] 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")

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

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