Package: RiboProfiling 1.42.0

A. Popa

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.

Authors:Alexandra Popa

RiboProfiling_1.42.0.tar.gz
RiboProfiling_1.42.0.zip(r-4.7-any)RiboProfiling_1.42.0.zip(r-4.6-any)RiboProfiling_1.42.0.zip(r-4.5-any)
RiboProfiling_1.42.0.tgz(r-4.6-any)RiboProfiling_1.42.0.tgz(r-4.5-any)
RiboProfiling_1.42.0.tar.gz(r-4.7-any)RiboProfiling_1.42.0.tar.gz(r-4.6-any)
RiboProfiling_1.42.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RiboProfiling/json (API)

# Install 'RiboProfiling' in R:
install.packages('RiboProfiling', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • cdsPosTransc - Per transcript relative position of start and end codons for dataset ctrlGAlignments
  • codonDataCtrl - Codon frequency and coverage in ORFs on chromosome 1, for dataset ctrlGAlignments
  • codonIndexCovCtrl - The read coverage for each codon in ORFs on chromosome 1, for dataset ctrlGAlignments
  • ctrlGAlignments - Ribosome profiling data on chr1 in human primary BJ fibroblasts control data: PMID: 23594524.

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

riboseqsequencingcoveragealignmentqualitycontrolsoftwareprincipalcomponent

2.48 score 10 scripts 11 mentions 12 exports 130 dependencies

Last updated from:7995c60f34 (on RELEASE_3_23). Checks:9 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR290
linux-develERROR700
source / vignettesERROR515
linux-releaseERROR639
macos-releaseERROR584
macos-oldrelERROR468
windows-develERROR541
windows-releaseERROR535
windows-oldrelERROR525
wasm-releaseOK230

Exports:aroundPromotercodonInfocodonPCAcountShiftReadscountsPlothistMatchLengthorfRelativePosplotSummarizedCovprintPCAreadStartCovreadsToStartOrEndriboSeqFromBAM

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatechroncigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbioggplot2gluegraphgridExtragsubfngtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslOrganismDbipkgconfigplyrpngProtGenericsprotoR6rappdirsRBGLRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraysqldfstringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Returns the flank size around the TSS for the x % CDSsaroundPromoter
Per transcript relative position of start and end codons for dataset ctrlGAlignmentscdsPosTransc
Codon frequency and coverage in ORFs on chromosome 1, for dataset ctrlGAlignmentscodonDataCtrl
The read coverage for each codon in ORFs on chromosome 1, for dataset ctrlGAlignmentscodonIndexCovCtrl
Associates the read counts on codons with the codon type for each ORF.codonInfo
PCA graphs on codon coveragecodonPCA
Apply an offset on the read start along the transcript and returns the coverage on the 5pUTR, CDS, 3pUTR, as well as a matrix of codon coverage per ORF.countShiftReads
Graphs of sample read counts (quality assesment)countsPlot
Ribosome profiling data on chr1 in human primary BJ fibroblasts control data: PMID: 23594524.ctrlGAlignments
Histogram of match length distribution of reads.histMatchLength
Relative position of the start and stop codon along the transcriptorfRelativePos
Plots the summarized coverage in a specified range (e.g. around TSS) for the specified match sizesplotSummarizedCov
Plots the PCA scatterplots produced by codonPCA function.printPCA
Read start coverage around the TSS on the predifined CDSsreadStartCov
Reads in GAlignments converted to either Read Start (5') or End (3') PositionsreadsToStartOrEnd
RiboProfiling.RiboProfiling-package RiboProfiling
Starting from a BAM file path: quality plots, shift ribosome position, coverage on multiple transcript features and on codons.riboSeqFromBAM