AssessORF
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see AssessORF.
Assess Gene Predictions Using Proteomics and Evolutionary Conservation
Bioconductor version: 3.9
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("AssessORF")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| Using AssessORF | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ComparativeGenomics, GenePrediction, Genetics, GenomeAnnotation, Proteomics, QualityControl, Software, Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), DECIPHER(>= 2.10.0) |
| Imports | Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | AssessORFData, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | AssessORFData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | AssessORF_1.2.0.tar.gz |
| Windows Binary | AssessORF_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | AssessORF_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/AssessORF |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AssessORF |
| Bioc Package Browser | https://code.bioconductor.org/browse/AssessORF/ |
| Package Short Url | https://bioconductor.org/packages/AssessORF/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |