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
Version1.3.2

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Files in this package

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/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/man
RiboProfiling/man/RiboProfiling.Rd RiboProfiling/man/aroundPromoter.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.

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