This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Basic4Cseq

This is the development version of Basic4Cseq; for the stable release version, see Basic4Cseq.

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

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("Basic4Cseq")):

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Alignment, Coverage, DataImport, ImmunoOncology, QualityControl, RNASeq, SequenceMatching, Sequencing, Software, Visualization
Version 1.37.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 years)
License LGPL-3
Depends R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils
Imports methods, RCircos, BSgenome.Ecoli.NCBI.20080805
Linking To
Suggests BSgenome.Hsapiens.UCSC.hg19
System Requirements
Enhances
URL
See More
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_1.37.0.tar.gz
Windows Binary Basic4Cseq_1.37.0.zip (64-bit only)
macOS Binary (x86_64) Basic4Cseq_1.37.0.tgz
macOS Binary (arm64) Basic4Cseq_1.37.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Basic4Cseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Basic4Cseq
Bioc Package Browser https://code.bioconductor.org/browse/Basic4Cseq/
Package Short Url https://bioconductor.org/packages/Basic4Cseq/
Package Downloads Report Download Stats