DOI: 10.18129/B9.bioc.FourCSeq    

Package analyse 4C sequencing data

Bioconductor version: Release (3.6)

FourCSeq is an R package dedicated to the analysis of (multiplexed) 4C sequencing data. The package provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions. The statistical analysis in R starts with individual bam files for each sample as inputs. To obtain these files, the package contains a python script (extdata/python/ to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.

Author: Felix A. Klein, EMBL Heidelberg

Maintainer: Felix A. Klein <daggoth at>

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biocViews Preprocessing, Sequencing, Software
Version 1.12.0
In Bioconductor since BioC 3.0 (R-3.1) (3.5 years)
License GPL (>= 3)
Depends R (>= 3.0), GenomicRanges, ggplot2, DESeq2(>= 1.9.11), splines, methods, LSD
Imports DESeq2, Biobase, Biostrings, GenomicRanges, SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer, fda, GenomicAlignments, gtools, Matrix
Suggests BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene
Depends On Me
Imports Me
Suggests Me
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