RiboProfiling: Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Version 1.6.0

Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.

Browse man pages Browse package API and functions Browse package files

AuthorAlexandra Popa
Bioconductor views Alignment Coverage PrincipalComponent QualityControl RiboSeq Sequencing Software
Date of publicationNone
MaintainerA. Popa <alexandra.mariela.popa@gmail.com>
LicenseGPL-3
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RiboProfiling")

Man pages

aroundPromoter: Returns the flank size around the TSS for the x % CDSs
cdsPosTransc: Per transcript relative position of start and end codons for...
codonDataCtrl: Codon frequency and coverage in ORFs on chromosome 1, for...
codonIndexCovCtrl: The read coverage for each codon in ORFs on chromosome 1, for...
codonInfo: Associates the read counts on codons with the codon type for...
codonPCA: PCA graphs on codon coverage
countShiftReads: Apply an offset on the read start along the transcript and...
countsPlot: Graphs of sample read counts (quality assesment)
ctrlGAlignments: Ribosome profiling data on chr1 in human primary BJ...
histMatchLength: Histogram of match length distribution of reads.
orfRelativePos: Relative position of the start and stop codon along the...
plotSummarizedCov: Plots the summarized coverage in a specified range (e.g....
printPCA: Plots the PCA scatterplots produced by codonPCA function.
readStartCov: Read start coverage around the TSS on the predifined CDSs
readsToStartOrEnd: Reads in GAlignments converted to either Read Start (5') or...
RiboProfiling: RiboProfiling.
riboSeqFromBAM: Starting from a BAM file path: quality plots, shift ribosome...

Functions

RiboProfiling Man page
RiboProfiling-package Man page
applyShiftFeature Source code
aroundPromoter Man page Source code
cdsPosTransc Man page
codonDataCtrl Man page
codonIndexCovCtrl Man page
codonInfo Man page Source code
codonPCA Man page Source code
countShiftReads Man page Source code
countsPlot Man page Source code
ctrlGAlignments Man page
funcBoxplot Source code
funcDataFrameGGPlot2 Source code
funcPlotPairs Source code
getCodons Source code
getSummarizedCov Source code
histMatchLength Man page Source code
makePairs Source code
naTozeroRle Source code
normRange Source code
orfRelativePos Man page Source code
plotSummarizedCov Man page Source code
printPCA Man page Source code
readStartCov Man page Source code
readStartCov1Aln Source code
readsToStartOrEnd Man page Source code
redefineStartEnd Source code
riboSeqFromBAM Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/aroundPromoter.R
R/codonInfo.R
R/codonPCA.R
R/countShiftReads.R
R/countsPlot.R
R/dataDescription.R
R/histMatchLength.R
R/orfRelativePos.R
R/plotSummarizedCov.R
R/printPCA.R
R/readStartCov.R
R/readsToStartOrEnd.R
R/riboSeqFromBAM.R
R/utils.R
build
build/vignette.rds
data
data/cdsPosTransc.rda
data/codonDataCtrl.rda
data/codonIndexCovCtrl.rda
data/ctrlGAlignments.rda
data/datalist
inst
inst/doc
inst/doc/RiboProfiling.R
inst/doc/RiboProfiling.Rnw
inst/doc/RiboProfiling.pdf
inst/extdata
inst/extdata/ctrl_sample.bam
inst/extdata/nutlin2h_sample.bam
man
man/RiboProfiling.Rd
man/aroundPromoter.Rd
man/cdsPosTransc.Rd
man/codonDataCtrl.Rd
man/codonIndexCovCtrl.Rd
man/codonInfo.Rd
man/codonPCA.Rd
man/countShiftReads.Rd
man/countsPlot.Rd
man/ctrlGAlignments.Rd
man/histMatchLength.Rd
man/orfRelativePos.Rd
man/plotSummarizedCov.Rd
man/printPCA.Rd
man/readStartCov.Rd
man/readsToStartOrEnd.Rd
man/riboSeqFromBAM.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test-aroundPromoter.R
tests/testthat/test-readStartCov.R
tests/testthat/test-riboSeqFromBAM.R
vignettes
vignettes/RiboProfiling.Rnw
RiboProfiling documentation built on May 20, 2017, 10:14 p.m.