fourSynergy

Ensemble algorithm for 4C-seq data

Bioconductor version: 3.23 · Package version: 1.0.0

fourSynergy is an ensemble algorithm leveraging synergies among the existing 4C-seq algorithms r3C-seq, peakC, r.4cker and fourSig. It uses a weighted voting approach to perform improved interaction calling. fourSynergy supports also differential interaction calling.

Installation

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

BiocManager::install("fourSynergy")

Details

Maintainer	Sophie Wind <sophie.wind@uni-muenster.de>
Author	Sophie Wind [aut, cre] (ORCID: <https://orcid.org/0009-0002-1174-8201>), Carolin Walter [aut, fnd] (ORCID: <https://orcid.org/0000-0002-5155-7728>)
License	LGPL-3
URL	https://github.com/sophiewind/fourSynergy
Bug Reports	https://github.com/sophiewind/fourSynergy/issues
Downloads rank	64
Source branch	RELEASE_3_23
biocViews	DifferentialPeakCalling, Sequencing, Software

Documentation

fourSynergy

Download

Source package

Dependencies

Depends: R (>= 4.5.0), GenomicRanges

Imports: magrittr, dplyr, ggplot2, tibble, org.Hs.eg.db, org.Mm.eg.db, reshape2, tidyr, methods, jsonlite, karyoploteR, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, bamsignals, DESeq2, GenomeInfoDb, graphics, stringr, yaml

Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle