AssessORF

DOI: 10.18129/B9.bioc.AssessORF    

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

Bioconductor version: Release (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>

Citation (from within R, enter citation("AssessORF")):

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("AssessORF", version = "3.8")

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
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
Old Source Packages for BioC 3.8 Source Archive

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