RiboProfiling
This package is for version 3.8 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: 3.8
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("RiboProfiling")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Coverage, PrincipalComponent, QualityControl, RiboSeq, Sequencing, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RiboProfiling_1.12.0.tar.gz |
| Windows Binary | RiboProfiling_1.12.0.zip |
| Mac OS X 10.11 (El Capitan) | RiboProfiling_1.12.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |