rmspc
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see rmspc.
Multiple Sample Peak Calling
Bioconductor version: 3.18
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("rmspc")):
Installation
To install this package, start R (version "4.3") 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")| User guide to the rmspc package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, ChipOnChip, DataImport, RNASeq, Sequencing, Software |
| Version | 1.8.0 |
| 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_1.8.0.tar.gz |
| Windows Binary | rmspc_1.8.0.zip (64-bit only) |
| macOS Binary (x86_64) | rmspc_1.8.0.tgz |
| macOS Binary (arm64) | rmspc_1.8.0.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 |