DOI: 10.18129/B9.bioc.Basic4Cseq  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Basic4Cseq.

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

Bioconductor version: 3.16

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 < at>

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


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


biocViews Alignment, Coverage, DataImport, ImmunoOncology, QualityControl, RNASeq, SequenceMatching, Sequencing, Software, Visualization
Version 1.34.0
In Bioconductor since BioC 2.14 (R-3.1) (9 years)
License LGPL-3
Depends R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils
Imports methods, RCircos, BSgenome.Ecoli.NCBI.20080805
Suggests BSgenome.Hsapiens.UCSC.hg19
Depends On Me
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