rmspc

DOI: 10.18129/B9.bioc.rmspc    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see rmspc.

Multiple Sample Peak Calling

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	ChIPSeq, ChipOnChip, DataImport, RNASeq, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
License	GPL-3
Depends
Imports	processx, BiocManager, rtracklayer, stats, tools, methods, GenomicRanges, stringr
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
SystemRequirements	.NET 5.0
Enhances
URL	https://genometric.github.io/MSPC/
BugReports	https://github.com/Genometric/MSPC/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	rmspc_1.2.0.tar.gz
Windows Binary	rmspc_1.2.0.zip
macOS Binary (x86_64)	rmspc_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rmspc
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rmspc
Package Short Url	https://bioconductor.org/packages/rmspc/
Package Downloads Report	Download Stats