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AssessORF

This is the development version of AssessORF; for the stable release version, see AssessORF.

Assess Gene Predictions Using Proteomics and Evolutionary Conservation


Bioconductor version: Development (3.19)

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 alumni.cmu.edu>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ComparativeGenomics, GenePrediction, Genetics, GenomeAnnotation, Proteomics, QualityControl, Software, Visualization
Version 1.21.0
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
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Suggests AssessORFData, BiocStyle, knitr, rmarkdown
Linking To
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Depends On Me
Imports Me
Suggests Me AssessORFData
Links To Me
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Package Archives

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

Source Package AssessORF_1.21.0.tar.gz
Windows Binary AssessORF_1.21.0.zip
macOS Binary (x86_64) AssessORF_1.21.0.tgz
macOS Binary (arm64) AssessORF_1.21.0.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