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 (3.24)
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("AssessORF")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ComparativeGenomics, GenePrediction, Genetics, GenomeAnnotation, Proteomics, QualityControl, Software, Visualization |
| Version | 1.31.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 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, RSQLite (>= 1.1) |
| 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_1.31.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | AssessORF_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | AssessORF_1.31.0.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 |