fourSynergy
This is the development version of fourSynergy; to use it, please install the devel version of Bioconductor.
Ensemble algorithm for 4C-seq data
Bioconductor version: Development (3.23)
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.
Author: Sophie Wind [aut, cre]
, Carolin Walter [aut, fnd]
Maintainer: Sophie Wind <sophie.wind at uni-muenster.de>
citation("fourSynergy")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("fourSynergy")
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("fourSynergy")| fourSynergy_vignette | HTML | R Script |
| Reference Manual |
Details
| biocViews | DifferentialPeakCalling, Sequencing, Software |
| Version | 0.99.12 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | LGPL-3 |
| 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 |
| System Requirements | |
| URL | https://github.com/sophiewind/fourSynergy |
| Bug Reports | https://github.com/sophiewind/fourSynergy/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle |
| 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 | fourSynergy_0.99.12.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/fourSynergy |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/fourSynergy |
| Bioc Package Browser | https://code.bioconductor.org/browse/fourSynergy/ |
| Package Short Url | https://bioconductor.org/packages/fourSynergy/ |
| Package Downloads Report | Download Stats |