Package: SingleMoleculeFootprinting
Title: Analysis tools for Single Molecule Footprinting (SMF) data
Version: 2.2.0
Authors@R: c(
    person(given = "Guido",
           family = "Barzaghi",
           role = c("aut", "cre"),
           email = "guido.barzaghi@embl.de",
           comment = c(ORCID = "0000-0001-6066-3920")),
    person(given = "Arnaud",
           family = "Krebs",
           role = c("aut"),
           email = "arnaud.krebs@embl.de",
           comment = c(ORCID = "0000-0001-7999-6127")),
    person(given = "Mike",
           family = "Smith",
           role = c("ctb"),
           email = "mike.smith@embl.de",
           comment = c(ORCID = "0000-0002-7800-3848"))
    )
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
Description: 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.
biocViews: DNAMethylation, Coverage, NucleosomePositioning,
        DataRepresentation, Epigenetics, MethylSeq, QualityControl,
        Sequencing
URL:
        https://www.bioconductor.org/packages/release/bioc/html/SingleMoleculeFootprinting.html
BugReports: https://github.com/Krebslabrep/SingleMoleculeFootprinting/issues
License: GPL-3
Encoding: UTF-8
Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr,
        qs, rmarkdown, readr, rrapply, SingleMoleculeFootprintingData,
        testthat (>= 3.0.0), tidyverse
VignetteBuilder: knitr
RoxygenNote: 7.3.2
Config/testthat/edition: 3
git_url:
        https://git.bioconductor.org/packages/SingleMoleculeFootprinting
git_branch: RELEASE_3_21
git_last_commit: a14d84c
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 03:52:44 UTC; biocbuild
Author: Guido Barzaghi [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-6066-3920>),
  Arnaud Krebs [aut] (ORCID: <https://orcid.org/0000-0001-7999-6127>),
  Mike Smith [ctb] (ORCID: <https://orcid.org/0000-0002-7800-3848>)
Maintainer: Guido Barzaghi <guido.barzaghi@embl.de>
Built: R 4.5.0; ; 2025-04-16 15:33:51 UTC; windows
