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

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.

Author
Julius Muller
Date of publication
None
Maintainer
Julius Muller <ju-mu@alumni.ethz.ch>
License
GPL-3
Version
1.18.0
URLs

View on Bioconductor

Man pages

annotatePeaks
Associates peaks to TSS
DensityContainer-class
Class '"DensityContainer"'
gtf2gr
GTF file parsing
histogram-methods
Histogram of the read distribution
macs2gr
Convenience function for MACS output conversion
meltPeak
Convenience function which returns a data frame with...
parseReads
User configurable efficient assembly of read density maps
peak2tss
Changes the peak center to the next TSS according to previous...
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...
TransView-package
Read density map construction and accession. Visualization of...
TVResults-class
Class '"TVResults"'
tvStats-methods
DensityContainer accessor function

Files in this package

TransView/.Rinstignore
TransView/DESCRIPTION
TransView/NAMESPACE
TransView/NEWS
TransView/R
TransView/R/TransView_AllClasses.R
TransView/R/TransView_AllGenerics.R
TransView/R/TransView_accessors.R
TransView/R/TransView_parseReads.R
TransView/R/TransView_plotTV.R
TransView/R/TransView_plotTVData.R
TransView/R/TransView_setter.R
TransView/R/TransView_show.R
TransView/R/TransView_slice.R
TransView/R/TransView_sliceT.R
TransView/R/TransView_tools.R
TransView/R/test_TransView_package.R
TransView/R/zzz.R
TransView/build
TransView/build/vignette.rds
TransView/inst
TransView/inst/doc
TransView/inst/doc/TransView.R
TransView/inst/doc/TransView.Rnw
TransView/inst/doc/TransView.pdf
TransView/inst/extdata
TransView/inst/extdata/dm3_chr4.gtf.gz
TransView/inst/extdata/example_ctrl_sam.bam
TransView/inst/extdata/example_mm9.gtf.gz
TransView/inst/extdata/example_sam.bam
TransView/inst/extdata/test.sam
TransView/inst/extdata/test_macs.xls
TransView/inst/unitTests
TransView/inst/unitTests/test_parseReads.R
TransView/inst/unitTests/test_slice.R
TransView/man
TransView/man/DensityContainer-class.Rd
TransView/man/TVResults-class.Rd
TransView/man/TransView-package.Rd
TransView/man/annotatePeaks.Rd
TransView/man/gtf2gr.Rd
TransView/man/histogram-methods.Rd
TransView/man/macs2gr.Rd
TransView/man/meltPeak.Rd
TransView/man/parseReads.Rd
TransView/man/peak2tss.Rd
TransView/man/plotTV.Rd
TransView/man/plotTVData.Rd
TransView/man/rmTV.Rd
TransView/man/slice1.Rd
TransView/man/slice1T.Rd
TransView/man/tvStats-methods.Rd
TransView/src
TransView/src/Makevars
TransView/src/Makevars.win
TransView/src/R_init_TransView.c
TransView/src/bin_density.c
TransView/src/bin_density.h
TransView/src/construct_dc.c
TransView/src/construct_dc.h
TransView/src/parse_sam.c
TransView/src/parse_sam.h
TransView/src/slice_dc.c
TransView/src/slice_dc.h
TransView/src/visuals.c
TransView/src/visuals.h
TransView/tests
TransView/tests/TransView_unit_tests.R
TransView/vignettes
TransView/vignettes/TransView.Rnw
TransView/vignettes/example_induced_top1k.png