AssessORF

DOI: 10.18129/B9.bioc.AssessORF    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see AssessORF.

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

Bioconductor version: 3.8

In order to assess the quality of a set of predicted genes for a genome, evidence must first be mapped to that genome. Next, each gene must be categorized based on how strong the evidence is for or against that gene. The AssessORF package provides the functions and class structures necessary for accomplishing those tasks, using proteomic hits and evolutionarily conserved start codons as the forms of evidence.

Author: Deepank Korandla [aut, cre], Erik Wright [aut]

Maintainer: Deepank Korandla <dkorandl at andrew.cmu.edu>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("AssessORF")

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("AssessORF")

 

PDF	R Script	Using AssessORF
PDF		Reference Manual

Details

biocViews	ComparativeGenomics, GenePrediction, Genetics, GenomeAnnotation, Proteomics, QualityControl, Software, Visualization
Version	1.0.2
In Bioconductor since	BioC 3.8 (R-3.5) (0.5 years)
License	GPL-3
Depends	R (>= 3.5.0), DECIPHER(>= 2.8.0)
Imports	Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils
LinkingTo
Suggests	AssessORFData, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	AssessORFData
Links To Me
Build Report

Package Archives

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

Source Package	AssessORF_1.0.2.tar.gz
Windows Binary	AssessORF_1.0.2.zip
Mac OS X 10.11 (El Capitan)	AssessORF_1.0.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AssessORF
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AssessORF
Package Short Url	http://bioconductor.org/packages/AssessORF/
Package Downloads Report	Download Stats