riboSeqR: Analysis of sequencing data from ribosome profiling experiments

Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("riboSeqR")
AuthorThomas J. Hardcastle
Bioconductor views Genetics RiboSeq Sequencing Visualization
Date of publicationNone
MaintainerThomas J. Hardcastle <tjh48@cam.ac.uk>
LicenseGPL-3
Version1.10.0

View on Bioconductor

Functions

filterHits Man page
findCDS Man page
frameCounting Man page
lengthDist Man page
libScales Man page
logoContext Man page
plotCDS Man page
plotFS Man page
plotTranscript Man page
readingFrame Man page
readRibodata Man page
riboCoding Man page
[,riboCoding,ANY,ANY-method Man page
[,riboCoding,ANY-method Man page
riboCoding-class Man page
[,riboCoding-method Man page
riboData Man page
riboData-class Man page
riboSeqR Man page
riboSeqR-package Man page
rnaCounts Man page
show,riboCoding-method Man page
sliceCounts Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/filterHits.R R/findCDS.R R/frameCounting.R R/frameShift.R R/lengthDist.R R/libScales.R R/logoContext.R R/plotCodons.R R/plotTranscript.R R/readRibodata.R R/riboCoding-methods.R R/riboSeq-internal.R R/sliceCounts.R R/tableOverlaps.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/riboSeqR.R
inst/doc/riboSeqR.Rnw
inst/doc/riboSeqR.pdf
inst/extdata
inst/extdata/chlamy236_plus_deNovo_plusOnly_Index10
inst/extdata/chlamy236_plus_deNovo_plusOnly_Index12
inst/extdata/chlamy236_plus_deNovo_plusOnly_Index14
inst/extdata/chlamy236_plus_deNovo_plusOnly_Index16
inst/extdata/chlamy236_plus_deNovo_plusOnly_Index17
inst/extdata/chlamy236_plus_deNovo_plusOnly_Index17_short
inst/extdata/chlamy236_plus_deNovo_plusOnly_Index3
inst/extdata/chlamy236_plus_deNovo_plusOnly_Index5
inst/extdata/chlamy236_plus_deNovo_plusOnly_Index7
inst/extdata/ribotable.txt
inst/extdata/rsem_chlamy236_deNovo.transcripts.fa
inst/extdata/unit_test.fasta
inst/unitTests
inst/unitTests/testing.R
man
man/filterHits.Rd man/findCDS.Rd man/frameCounting.Rd man/frameShift.Rd man/lengthDist.Rd man/libScales.Rd man/logoContext.Rd man/plotCDS.Rd man/plotTranscript.Rd man/readRibodata.Rd man/riboCoding-class.Rd man/riboData-class.Rd man/riboSeqR-package.Rd man/rnaCounts.Rd man/sliceCounts.Rd
tests
tests/runTests.R
vignettes
vignettes/_TZ_14128-node7-plantsci-internal-cam-ac-uk.tex
vignettes/riboSeqR.Rnw

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

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