FourCSeq

DOI:10.18129/B9.bioc.FourCSeq

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, seeFourCSeq.

Package analyse 4C sequencing data

Bioconductor version: 3.9

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("FourCSeq")

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("FourCSeq")

PDF	R Script	FourCSeq
PDF		Reference Manual

Details

biocViews	Preprocessing,Sequencing,Software
Version	1.18.0
In Bioconductor since	BioC 3.0 (R-3.1) (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

Package Archives

Followbob 体育网址 instructions to use this package in your R session.

Source Package	FourCSeq_1.18.0.tar.gz
Windows Binary	FourCSeq_1.18.0.zip(32- & 64-bit)
Mac OS X 10.11 (El Capitan)	FourCSeq_1.18.0.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	//www.anjoumacpherson.com/packages/FourCSeq/
Package Downloads Report	Download Stats