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Bioconductor - RiboProfiling (development version)

RiboProfiling

This is the development version of RiboProfiling; for the stable release version, see RiboProfiling.

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

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RiboProfiling")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RiboProfiling")
Analysing Ribo-Seq data with the "RiboProfiling" package PDF R Script Reference Manual PDF NEWS Text Details biocViews Alignment, Coverage, PrincipalComponent, QualityControl, RiboSeq, Sequencing, Software Version 1.39.0 In Bioconductor since BioC 3.2 (R-3.2) (9.5 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 System Requirements URL See More Package Archives

Follow Installation instructions to use this package in your R session.

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