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TransView (version 1.16.0)

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.

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Version

Version

1.16.0

License

GPL-3

Maintainer

Julius Muller

Last Published

February 15th, 2017

Functions in TransView (1.16.0)

TVResults-class

Class "TVResults"
slice1

Slice read densities from a TransView dataset
slice1T

Slice read densities of whole transcripts from a TransView DensityContainer
meltPeak

Convenience function which returns a data frame with normalized peak densities suitable for plotting with ggplot2
plotTVData

Summarize plotTV results
peak2tss

Changes the peak center to the next TSS according to previous annotation
plotTV

Plot and cluster global read densities
histogram-methods

Histogram of the read distribution
annotatePeaks

Associates peaks to TSS
parseReads

User configurable efficient assembly of read density maps
gtf2gr

GTF file parsing
macs2gr

Convenience function for MACS output conversion
tvStats-methods

DensityContainer accessor function
TransView-package

Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets.
DensityContainer-class

Class "DensityContainer"
rmTV

Free space occupied by DensityContainer