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RiboProfiling
This is thereleased version of RiboProfiling; for the devel version, seeRiboProfiling.
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Bioconductor version: Release (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("RiboProfiling")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("RiboProfiling")For older versions of R, please refer to the appropriateBioconductor 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 | 1.39.1 |
| In Bioconductor since | BioC 3.2 (R-3.2) (10 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0),Biostrings |
| Imports | methods,BiocGenerics,Seqinfo,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
FollowInstallation instructions to use this package in your R session.
| Source Package | RiboProfiling_1.39.1.tar.gz |
| Windows Binary (x86_64) | RiboProfiling_1.39.1.zip |
| macOS Binary (x86_64) | RiboProfiling_1.39.1.tgz |
| macOS Binary (arm64) | RiboProfiling_1.39.1.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 |