rmspc
This is the released version of rmspc; for the devel version, see rmspc.
All Bioconductor versions of rmspc
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14
Multiple Sample Peak Calling
Bioconductor version: 3.23 · Package version: 1.18.0
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"):
Vahid Jalili, Marzia Angela Cremona, Fernando Palluzzi, Meriem Bahda. rmspc: Multiple Sample Peak Calling. doi:10.18129/B9.bioc.rmspc, R package version 1.18.0, https://bioconductor.org/packages/rmspc.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.18.0 |
| License | GPL-3 |
| URL | https://genometric.github.io/MSPC/ |
| Bug Reports | https://github.com/Genometric/MSPC/issues |
| System Requirements | .NET 9.0 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 years) |
| Downloads rank | 1818 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ChIPSeq, ChipOnChip, DataImport, RNASeq, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/rmspc/ |
Documentation
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | rmspc_1.18.0.tar.gz |
| Windows binary (x86_64) | rmspc_1.17.0.zip |
| macOS binary (arm64) | rmspc_1.18.0.tgz |
| macOS binary (x86_64) | rmspc_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rmspc |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rmspc |
| Package Downloads Report | Download Stats |
Dependencies
Imports: processx, BiocManager, rtracklayer, stats, tools, methods, GenomicRanges, stringr
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)