DOI: 10.18129/B9.bioc.RiboProfiling  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see RiboProfiling.

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

Bioconductor version: 3.16

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>

Citation (from within R, enter citation("RiboProfiling")):


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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 1.28.0
In Bioconductor since BioC 3.2 (R-3.2) (7.5 years)
License GPL-3
Depends R (>= 3.5.0), 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
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package RiboProfiling_1.28.0.tar.gz
Windows Binary RiboProfiling_1.28.0.zip (64-bit only)
macOS Binary (x86_64) RiboProfiling_1.28.0.tgz
macOS Binary (arm64) RiboProfiling_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RiboProfiling
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RiboProfiling
Bioc Package Browser https://code.bioconductor.org/browse/RiboProfiling/
Package Short Url https://bioconductor.org/packages/RiboProfiling/
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