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Bioconductor - Basic4Cseq (development version)

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 (3.22)

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 "4.5") 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 1.45.1 In Bioconductor since BioC 2.14 (R-3.1) (11 years) License LGPL-3 Depends R (>= 3.5.0), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports methods, RCircos, BSgenome.Ecoli.NCBI.20080805 System Requirements URL See More Package Archives

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

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