TransView-package {TransView} | R Documentation

## Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets.

### Description

This package provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.

### Details

Package: | TransView
Type: | Package
Version: | 1.7.4
URL: | http://bioconductor.org/packages/release/bioc/html/TransView.html
License: | GPL-3
LazyLoad: | yes
Depends: | methods,GenomicRanges
Imports: | Rsamtools,zlibbioc,gplots,IRanges
Suggests: | RUnit,pasillaBamSubset
biocViews: | Bioinformatics,DNAMethylation,GeneExpression,Transcription, Microarray,Sequencing,HighThroughputSequencing,ChIPseq,RNAseq, Methylseq,DataImport,Visualization,Clustering,MultipleComparisons
LinkingTo: | Rsamtools

Index:

    DensityContainer-class
                            Class '"DensityContainer"'
    TVResults-class         Class '"TVResults"'
    TransView-package       The TransView package: Construction and
                            visualisation of read density maps.
    annotatePeaks           Associates peaks to TSS
    gtf2gr                  GTF file parsing
    histogram-methods       Histogram of the read distribution
    macs2gr                 Convenience function for MACS output conversion
    parseReads              User configurable efficient assembly of read
                            density maps
    peak2tss                Changes the peak center to the TSS
    plotTV                  Plot and cluster global read densities
    plotTVData              Summarize plotTV results
    rmTV                    Free space occupied by DensityContainer
    slice1                  Slice read densities from a TransView dataset
    slice1T                 Slice read densities of whole transcripts from
                            a TransView DensityContainer
    tvStats-methods         DensityContainer accessor function

Further information is available in the following vignettes:

`TransView` | An introduction to TransView (source, pdf)

### Author(s)

Julius Muller

Maintainer: Julius Muller <ju-mu@alumni.ethz.ch>

### Examples

    #see vignette

[Package TransView version 1.26.1 Index]