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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("TransView")
AuthorJulius Muller
Bioconductor views ChIPSeq Clustering DNAMethylation DataImport GeneExpression MethylSeq Microarray MultipleComparison RNASeq Sequencing Transcription Visualization
Date of publicationNone
MaintainerJulius Muller <ju-mu@alumni.ethz.ch>
LicenseGPL-3
Version1.20.0
http://bioconductor.org/packages/release/bioc/html/TransView.html

View on Bioconductor

Functions

annotatePeaks Man page
chromosomes Man page
chromosomes,DensityContainer-method Man page
class:DensityContainer Man page
class:TVResults Man page
cluster_order Man page
cluster_order,TVResults-method Man page
clusters Man page
clusters,TVResults-method Man page
collapsed Man page
collapsed,DensityContainer-method Man page
compression Man page
compression,DensityContainer-method Man page
data_pointer Man page
data_pointer,DensityContainer-method Man page
DensityContainer-class Man page
env Man page
env,DensityContainer-method Man page
ex_name Man page
ex_name<- Man page
ex_name<-,DensityContainer-method Man page
ex_name,DensityContainer-method Man page
filtered Man page
filtered,DensityContainer-method Man page
filtered_reads Man page
filtered_reads,DensityContainer-method Man page
fmapmass Man page
fmapmass,DensityContainer-method Man page
gcoverage Man page
gcoverage,DensityContainer-method Man page
gsize Man page
gsize,DensityContainer-method Man page
gtf2gr Man page
histogram Man page
histogram,DensityContainer-method Man page
histogram-methods Man page
lcoverage Man page
lcoverage,DensityContainer-method Man page
lmaxScore Man page
lmaxScore,DensityContainer-method Man page
lowqual Man page
lowqual,DensityContainer-method Man page
lsize Man page
lsize,DensityContainer-method Man page
macs2gr Man page
maxScore Man page
maxScore,DensityContainer-method Man page
meltPeak Man page
neg Man page
neg,DensityContainer-method Man page
nreads Man page
nreads,DensityContainer-method Man page
origin Man page
origin,DensityContainer-method Man page
paired Man page
paired,DensityContainer-method Man page
paired_reads Man page
paired_reads,DensityContainer-method Man page
parameters Man page
parameters,TVResults-method Man page
parseReads Man page
peak2tss Man page
plotTV Man page
plotTVData Man page
plotTVData-methods Man page
plotTVData,TVResults Man page
plotTVData,TVResults-method Man page
pos Man page
pos,DensityContainer-method Man page
proper_pairs Man page
proper_pairs,DensityContainer-method Man page
readthrough_pairs Man page
readthrough_pairs,DensityContainer-method Man page
rmTV Man page
rmTV,DensityContainer-method Man page
rmTV-methods Man page
scores_peaks Man page
scores_peaks,TVResults-method Man page
scores_rna Man page
scores_rna,TVResults-method Man page
show,DensityContainer-method Man page
show,TVResults-method Man page
size Man page
size,DensityContainer-method Man page
slice1 Man page
slice1,DensityContainer,character,numeric,numeric-method Man page
slice1-methods Man page
slice1T Man page
slice1T,DensityContainer,character-method Man page
slice1T-methods Man page
sliceN Man page
sliceN,DensityContainer-method Man page
sliceN-methods Man page
sliceNT Man page
sliceNT,DensityContainer,character-method Man page
sliceNT-methods Man page
spliced Man page
spliced<- Man page
spliced<-,DensityContainer-method Man page
spliced,DensityContainer-method Man page
strands Man page
strands,DensityContainer-method Man page
summaryTV Man page
summaryTV,TVResults-method Man page
TransView Man page
TransView-package Man page
TVResults-class Man page
tvStats Man page
tvStats,DensityContainer-method Man page
tvStats-methods Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.