FourCSeq
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see FourCSeq.
Package analyse 4C sequencing data
Bioconductor version: 3.11
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 [aut], Mike Smith [cre]
Maintainer: Mike Smith <mike.smith at embl.de>
citation("FourCSeq")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("FourCSeq")
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("FourCSeq")| FourCSeq | R Script | |
| Reference Manual |
Details
| biocViews | Preprocessing, Sequencing, Software |
| Version | 1.22.1 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 3.0), splines, LSD, DESeq2(>= 1.9.11), ggplot2 |
| Imports | Biobase, Biostrings, GenomicRanges, SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer, fda, GenomicAlignments, gtools, Matrix, methods |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene |
| 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 | FourCSeq_1.22.1.tar.gz |
| Windows Binary | FourCSeq_1.22.1.zip |
| macOS 10.13 (High Sierra) | FourCSeq_1.22.1.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 | https://bioconductor.org/packages/FourCSeq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |