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Basic4Cseq

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


Bioconductor version: Release (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")

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 1.38.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License LGPL-3
Depends R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils
Imports methods, RCircos, BSgenome.Ecoli.NCBI.20080805
System Requirements
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Suggests BSgenome.Hsapiens.UCSC.hg19
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Package Archives

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

Source Package Basic4Cseq_1.38.0.tar.gz
Windows Binary Basic4Cseq_1.38.0.zip
macOS Binary (x86_64) Basic4Cseq_1.38.0.tgz
macOS Binary (arm64) Basic4Cseq_1.38.0.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