Basic4Cseq

DOI: 10.18129/B9.bioc.Basic4Cseq    

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Bioconductor version: Release (3.14)

Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

Author: Carolin Walter

Maintainer: Carolin Walter <carolin.walter at uni-muenster.de>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Basic4Cseq")

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("Basic4Cseq")

 

PDF	R Script	Basic4Cseq: an R/Bioconductor package for the analysis of 4C-seq data
PDF		Reference Manual

Details

biocViews	Alignment, Coverage, DataImport, ImmunoOncology, QualityControl, RNASeq, SequenceMatching, Sequencing, Software, Visualization
Version	1.30.0
In Bioconductor since	BioC 2.14 (R-3.1) (8 years)
License	LGPL-3
Depends	R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils
Imports	methods, RCircos, BSgenome.Ecoli.NCBI.20080805
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Basic4Cseq_1.30.0.tar.gz
Windows Binary	Basic4Cseq_1.30.0.zip
macOS 10.13 (High Sierra)	Basic4Cseq_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Basic4Cseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Basic4Cseq
Package Short Url	https://bioconductor.org/packages/Basic4Cseq/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive