DOI: 10.18129/B9.bioc.rmspc  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see rmspc.

Multiple Sample Peak Calling

Bioconductor version: 3.17

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")):


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biocViews ChIPSeq, ChipOnChip, DataImport, RNASeq, Sequencing, Software
Version 1.6.0
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License GPL-3
Imports processx, BiocManager, rtracklayer, stats, tools, methods, GenomicRanges, stringr
Suggests knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
SystemRequirements .NET 6.0
URL https://genometric.github.io/MSPC/
BugReports https://github.com/Genometric/MSPC/issues
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