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

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.

AuthorAlexandra Popa
Date of publicationNone
MaintainerA. Popa <alexandra.mariela.popa@gmail.com>
LicenseGPL-3
Version1.4.1

View on Bioconductor

Functions

aroundPromoter Man page
cdsPosTransc Man page
codonDataCtrl Man page
codonIndexCovCtrl Man page
codonInfo Man page
codonPCA Man page
countShiftReads Man page
countsPlot Man page
ctrlGAlignments Man page
histMatchLength Man page
orfRelativePos Man page
plotSummarizedCov Man page
printPCA Man page
readStartCov Man page
readsToStartOrEnd Man page
RiboProfiling Man page
RiboProfiling-package Man page
riboSeqFromBAM Man page

Files

RiboProfiling/DESCRIPTION
RiboProfiling/NAMESPACE
RiboProfiling/NEWS
RiboProfiling/R
RiboProfiling/R/aroundPromoter.R RiboProfiling/R/codonInfo.R RiboProfiling/R/codonPCA.R RiboProfiling/R/countShiftReads.R RiboProfiling/R/countsPlot.R RiboProfiling/R/dataDescription.R RiboProfiling/R/histMatchLength.R RiboProfiling/R/orfRelativePos.R RiboProfiling/R/plotSummarizedCov.R RiboProfiling/R/printPCA.R RiboProfiling/R/readStartCov.R RiboProfiling/R/readsToStartOrEnd.R RiboProfiling/R/riboSeqFromBAM.R RiboProfiling/R/utils.R
RiboProfiling/build
RiboProfiling/build/vignette.rds
RiboProfiling/data
RiboProfiling/data/cdsPosTransc.rda
RiboProfiling/data/codonDataCtrl.rda
RiboProfiling/data/codonIndexCovCtrl.rda
RiboProfiling/data/ctrlGAlignments.rda
RiboProfiling/data/datalist
RiboProfiling/inst
RiboProfiling/inst/doc
RiboProfiling/inst/doc/RiboProfiling.R
RiboProfiling/inst/doc/RiboProfiling.Rnw
RiboProfiling/inst/doc/RiboProfiling.pdf
RiboProfiling/inst/extdata
RiboProfiling/inst/extdata/ctrl_sample.bam
RiboProfiling/inst/extdata/nutlin2h_sample.bam
RiboProfiling/man
RiboProfiling/man/RiboProfiling.Rd RiboProfiling/man/aroundPromoter.Rd RiboProfiling/man/cdsPosTransc.Rd RiboProfiling/man/codonDataCtrl.Rd RiboProfiling/man/codonIndexCovCtrl.Rd RiboProfiling/man/codonInfo.Rd RiboProfiling/man/codonPCA.Rd RiboProfiling/man/countShiftReads.Rd RiboProfiling/man/countsPlot.Rd RiboProfiling/man/ctrlGAlignments.Rd RiboProfiling/man/histMatchLength.Rd RiboProfiling/man/orfRelativePos.Rd RiboProfiling/man/plotSummarizedCov.Rd RiboProfiling/man/printPCA.Rd RiboProfiling/man/readStartCov.Rd RiboProfiling/man/readsToStartOrEnd.Rd RiboProfiling/man/riboSeqFromBAM.Rd
RiboProfiling/tests
RiboProfiling/tests/testthat
RiboProfiling/tests/testthat.R
RiboProfiling/tests/testthat/test-aroundPromoter.R
RiboProfiling/tests/testthat/test-readStartCov.R
RiboProfiling/tests/testthat/test-riboSeqFromBAM.R
RiboProfiling/vignettes
RiboProfiling/vignettes/RiboProfiling.Rnw

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.