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

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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.

Author
Alexandra Popa
Date of publication
None
Maintainer
A. Popa <alexandra.mariela.popa@gmail.com>
License
GPL-3
Version
1.3.2

View on Bioconductor

Man pages

aroundPromoter
Returns the flank size around the TSS for the x % CDSs
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...

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