DOI: 10.18129/B9.bioc.RiboProfiling    

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

Bioconductor version: Release (3.6)

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

Maintainer: A. Popa <alexandra.mariela.popa at gmail.com>

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PDF R Script Analysing Ribo-Seq data with the "RiboProfiling" package
PDF   Reference Manual
Text   NEWS


biocViews Alignment, Coverage, PrincipalComponent, QualityControl, RiboSeq, Sequencing, Software
Version 1.7.2
In Bioconductor since BioC 3.2 (R-3.2) (2.5 years)
License GPL-3
Depends R (>= 3.2.2), Biostrings
Imports BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2, GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments, ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf
Suggests knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment
Depends On Me
Imports Me
Suggests Me
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Source Package RiboProfiling_1.7.2.tar.gz
Windows Binary RiboProfiling_1.7.2.zip
Mac OS X 10.11 (El Capitan) RiboProfiling_1.7.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/RiboProfiling
Package Short Url http://bioconductor.org/packages/RiboProfiling/
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