TransView-package: Read density map construction and accession. Visualization of...

In TransView: 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:	zlibbioc,gplots,IRanges
Suggests:	RUnit,pasillaBamSubset
biocViews:	Bioinformatics,DNAMethylation,GeneExpression,Transcription, Microarray,Sequencing,HighThroughputSequencing,ChIPseq,RNAseq, Methylseq,DataImport,Visualization,Clustering,MultipleComparisons
LinkingTo:	Rhtslib

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 <[e-mail]>

Examples

#see vignette

Example output

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Welcome to TransView version 1.20.0

Attaching package: 'TransView'

The following object is masked from 'package:GenomicRanges':

    pos

TransView documentation built on Nov. 8, 2020, 5:31 p.m.