| TransView-package {TransView} | R Documentation |
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.
| 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) |
Julius Muller
Maintainer: Julius Muller <ju-mu@alumni.ethz.ch>
#see vignette