RiboProfiling
This is the released version of RiboProfiling; for the devel version, see RiboProfiling.
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Bioconductor version: Release (3.20)
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")
):
Popa A (2024). RiboProfiling: Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation. R package version 1.36.0.
Installation
To install this package, start R (version "4.4") 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 | 1.36.0 |
In Bioconductor since | BioC 3.2 (R-3.2) (9 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
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_1.36.0.tar.gz |
Windows Binary (x86_64) | RiboProfiling_1.36.0.zip |
macOS Binary (x86_64) | RiboProfiling_1.36.0.tgz |
macOS Binary (arm64) | RiboProfiling_1.36.0.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 |