Package: rmspc
Type: Package
Title: Multiple Sample Peak Calling
Version: 1.16.0
Authors@R: c(person("Vahid", "Jalili", role = "aut",  
                     email = "jalili.vahid@gmail.com"),  
             person("Marzia Angela", "Cremona", role = "aut",  
                     email = "marzia.cremona@fsa.ulaval.ca"), 
             person("Fernando", "Palluzzi", role = "aut", 
                     email = "fernando.palluzzi@gmail.com"),
             person("Meriem", "Bahda", role = c("aut","cre"),  
                     email = "meriembahda@gmail.com"))
Imports: processx, BiocManager, rtracklayer, stats, tools, methods,
        GenomicRanges, stringr
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
VignetteBuilder: knitr
Description: The rmspc package runs MSPC (Multiple Sample Peak Calling)
        software using R. The analysis of ChIP-seq samples outputs a
        number of enriched regions (commonly known as "peaks"), each
        indicating a protein-DNA interaction or a specific chromatin
        modification. When replicate samples are analyzed, overlapping
        peaks are expected. This repeated evidence can therefore be
        used to locally lower the minimum significance required to
        accept a peak. MSPC uses combined evidence from replicated
        experiments to evaluate peak calling output, rescuing peaks,
        and reduce false positives. It takes any number of replicates
        as input and improves sensitivity and specificity of peak
        calling on each, and identifies consensus regions between the
        input samples.
biocViews: ChIPSeq, Sequencing, ChipOnChip, DataImport, RNASeq
License: GPL-3
Encoding: UTF-8
URL: https://genometric.github.io/MSPC/
BugReports: https://github.com/Genometric/MSPC/issues
SystemRequirements: .NET 9.0
RoxygenNote: 7.1.1
Config/testthat/edition: 3
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:11:37 UTC
RemoteUrl: https://github.com/bioc/rmspc
RemoteRef: RELEASE_3_22
RemoteSha: 28a622eec694e71a02593d09aaf5aa0395bc31b0
NeedsCompilation: no
Packaged: 2025-11-12 10:29:44 UTC; root
Author: Vahid Jalili [aut],
  Marzia Angela Cremona [aut],
  Fernando Palluzzi [aut],
  Meriem Bahda [aut, cre]
Maintainer: Meriem Bahda <meriembahda@gmail.com>
Built: R 4.5.2; ; 2025-11-12 10:32:04 UTC; windows
