Package: fourSynergy 1.1.0

Sophie Wind

fourSynergy: Ensemble algorithm for 4C-seq data

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.

Authors:Sophie Wind [aut, cre], Carolin Walter [aut, fnd]

fourSynergy_1.1.0.tar.gz
fourSynergy_1.1.0.zip(r-4.7)fourSynergy_1.1.0.zip(r-4.6)fourSynergy_1.1.0.zip(r-4.5)
fourSynergy_1.1.0.tgz(r-4.6-any)fourSynergy_1.1.0.tgz(r-4.5-any)
fourSynergy_1.1.0.tar.gz(r-4.7-any)fourSynergy_1.1.0.tar.gz(r-4.6-any)
fourSynergy_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fourSynergy/json (API)

# Install 'fourSynergy' in R:

install.packages('fourSynergy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sophiewind/foursynergy/issues

On BioConductor:fourSynergy-1.1.0(bioc 3.24)fourSynergy-1.0.0(bioc 3.23)

sequencing software differentialpeakcalling

4.70 score 182 downloads 9 exports 140 dependencies

Last updated from:8ee7081853. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	309
linux-devel-x86_64	OK	649
source / vignettes	OK	529
linux-release-x86_64	OK	707
macos-release-arm64	OK	344
macos-oldrel-arm64	OK	492
windows-devel	OK	546
windows-release	OK	604
windows-oldrel	OK	625
wasm-release	OK	302

Exports:checkConfig consensusIa createIa differentialAnalysis plotBaseTracks plotConsensusIa plotConsensusTracks plotDiffIa plotIaIndiviualTools

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports bamsignals base64enc bezier BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DESeq2 dichromat digest dplyr ensembldb evaluate farver fastmap fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite karyoploteR KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle locfit magrittr Matrix MatrixGenerics matrixStats memoise mime nnet openssl org.Hs.eg.db org.Mm.eg.db pillar pkgconfig plyr png ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl regioneR reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML XVector yaml

fourSynergy

Rendered fromfourSynergy_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-03-06
Started: 2025-10-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
fourSynergy: Ensemble based interaction calling in 4C-seq data	fourSynergy-package fourSynergy
checkConfig	checkConfig
consensusIa	consensusIa
createIa	createIa
differentialAnalysis	differentialAnalysis
fourSynergy Class	fourSynergy-class
plotBaseTracks	plotBaseTracks
plotConsensusIa	plotConsensusIa
plotConsensusTracks	plotConsensusTracks
plotDiffIa	plotDiffIa
This function creates a karyoplot with the interactions calls of the individual tools.	plotIaIndiviualTools