Package: RiboProfiling 1.35.0
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:
RiboProfiling_1.35.0.tar.gz
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RiboProfiling_1.35.0.tgz(r-4.4-any)RiboProfiling_1.35.0.tgz(r-4.3-any)
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RiboProfiling.pdf |RiboProfiling.html✨
RiboProfiling/json (API)
NEWS
# Install 'RiboProfiling' in R: |
install.packages('RiboProfiling', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- 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 BioConductor:RiboProfiling-1.35.0(bioc 3.20)RiboProfiling-1.34.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:0a5feaaa7f
Exports:aroundPromotercodonInfocodonPCAcountShiftReadscountsPlothistMatchLengthorfRelativePosplotSummarizedCovprintPCAreadStartCovreadsToStartOrEndriboSeqFromBAM
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobbroombroom.helpersBSgenomebslibcachemcheckmatechronclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggbioggplot2ggstatsgluegraphgridExtragsubfngtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglabelledlambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslOrganismDbipatchworkpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericsprotopurrrR6rappdirsRBGLRColorBrewerRcppRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraysqldfstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2XVectoryamlzlibbioc