Basic4Cseq
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Basic4Cseq.
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Bioconductor version: 3.9
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("Basic4Cseq")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual |
Details
| biocViews | Alignment, Coverage, DataImport, ImmunoOncology, QualityControl, RNASeq, SequenceMatching, Sequencing, Software, Visualization |
| Version | 1.20.0 |
| 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 | |
| URL |
See More
| Suggests | BSgenome.Hsapiens.UCSC.hg19 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Basic4Cseq_1.20.0.tar.gz |
| Windows Binary | Basic4Cseq_1.20.0.zip |
| Mac OS X 10.11 (El Capitan) | Basic4Cseq_1.20.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |