This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see FourCSeq.
Bioconductor version: 3.8
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/demultiplex.py) 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 gmx.de>
Citation (from within R,
enter citation("FourCSeq")
):
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("FourCSeq")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("FourCSeq")
R Script | FourCSeq | |
Reference Manual |
biocViews | Preprocessing, Sequencing, Software |
Version | 1.16.0 |
In Bioconductor since | BioC 3.0 (R-3.1) (4.5 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 |
LinkingTo | |
Suggests | BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | FourCSeq_1.16.0.tar.gz |
Windows Binary | FourCSeq_1.16.0.zip |
Mac OS X 10.11 (El Capitan) | FourCSeq_1.16.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/FourCSeq |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/FourCSeq |
Package Short Url | http://bioconductor.org/packages/FourCSeq/ |
Package Downloads Report | Download Stats |
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