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:
Maintainer: Guido Barzaghi <guido.barzaghi at embl.de>
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
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 |
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 |
See More
| Suggests | BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, qs, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) |
| 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.
| Source Package | SingleMoleculeFootprinting_2.1.0.tar.gz |
| Windows Binary (x86_64) | SingleMoleculeFootprinting_2.1.0.zip |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/SingleMoleculeFootprinting/ |
| Package Short Url | https://bioconductor.org/packages/SingleMoleculeFootprinting/ |
| Package Downloads Report | Download Stats |