riboSeqR: Analysis of sequencing data from ribosome profiling experiments

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

Author
Thomas J. Hardcastle
Date of publication
None
Maintainer
Thomas J. Hardcastle <tjh48@cam.ac.uk>
License
GPL-3
Version
1.8.0

View on Bioconductor

Man pages

filterHits
Filters framecalled data based on the mean number of hits...
findCDS
Parses a transcriptome file looking for start/stop codons in...
frameCounting
Counts aligned reads within coding sequence regions by frame...
frameShift
Analyses frame called ribosome footprint data within coding...
lengthDist
A function plotting the density of lengths in a riboData...
libScales
Generates library scaling factors from ribosome footprint...
plotCDS
Plots average ribosome footprint alignment to coding...
plotTranscript
Plots ribosome footprint abundance and mRNA coverage (if...
readRibodata
Reads ribosomal and (optionally) rna data from alignment...
riboCoding-class
Class "riboCoding"
riboData-class
Class "riboData"
riboSeqR-package
Analysis of sequencing data from ribosome profiling...
rnaCounts
Extracts mRNA counts from a riboDat object for a set of...
sliceCounts
Slices out count data from riboCoding object for use in...

Files in this package

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