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rmspc

This is the development version of rmspc; for the stable release version, see rmspc.

Multiple Sample Peak Calling


Bioconductor version: Development (3.19)

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.

Author: Vahid Jalili [aut], Marzia Angela Cremona [aut], Fernando Palluzzi [aut], Meriem Bahda [aut, cre]

Maintainer: Meriem Bahda <meriembahda at gmail.com>

Citation (from within R, enter citation("rmspc")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("rmspc")

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("rmspc")
User guide to the rmspc package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, ChipOnChip, DataImport, RNASeq, Sequencing, Software
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends
Imports processx, BiocManager, rtracklayer, stats, tools, methods, GenomicRanges, stringr
System Requirements .NET 6.0
URL https://genometric.github.io/MSPC/
Bug Reports https://github.com/Genometric/MSPC/issues
See More
Suggests knitr, rmarkdown, BiocStyle, 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 rmspc_1.9.0.tar.gz
Windows Binary rmspc_1.9.0.zip (64-bit only)
macOS Binary (x86_64) rmspc_1.9.0.tgz
macOS Binary (arm64) rmspc_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rmspc
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rmspc
Bioc Package Browser https://code.bioconductor.org/browse/rmspc/
Package Short Url https://bioconductor.org/packages/rmspc/
Package Downloads Report Download Stats