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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RiboProfiling")
In most cases, you don't need to download the package archive at all.
RiboProfiling
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Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Bioconductor version: Release (3.4)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RiboProfiling")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RiboProfiling")
| R Script | Analysing Ribo-Seq data with the "RiboProfiling" package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, Coverage, PrincipalComponent, QualityControl, RiboSeq, Sequencing, Software |
| Version | 1.4.1 |
| In Bioconductor since | BioC 3.2 (R-3.2) (1.5 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 |
| LinkingTo | |
| Suggests | knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RiboProfiling_1.4.1.tar.gz |
| Windows Binary | RiboProfiling_1.4.1.zip |
| Mac OS X 10.9 (Mavericks) | RiboProfiling_1.4.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/RiboProfiling/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/RiboProfiling/ |
| Package Downloads Report | Download Stats |
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