Basic4Cseq
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Bioconductor version: 3.24 · Package version: 1.49.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Basic4Cseq")Details
| Maintainer | Carolin Walter <carolin.walter@uni-muenster.de> |
| Author | Carolin Walter |
| License | LGPL-3 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Coverage, DataImport, ImmunoOncology, QualityControl, RNASeq, SequenceMatching, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/Basic4Cseq/ |
Citation
From within R, enter citation("Basic4Cseq"):
Carolin Walter. Basic4Cseq: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data. doi:10.18129/B9.bioc.Basic4Cseq, R package version 1.49.0, https://bioconductor.org/packages/Basic4Cseq.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | Basic4Cseq_1.49.0.tar.gz |
| Windows binary (x86_64) | Basic4Cseq_1.49.0.zip |
| macOS binary (arm64) | Basic4Cseq_1.49.0.tgz |
| macOS binary (x86_64) | Basic4Cseq_1.49.0.tgz |
Dependencies
Depends: R (>= 3.5.0), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils
Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805
Suggests: BSgenome.Hsapiens.UCSC.hg19