AlphaMissenseR
This is the released version of AlphaMissenseR; for the devel version, see AlphaMissenseR.
Accessing AlphaMissense Data Resources in R
Bioconductor version: Release (3.23)
The AlphaMissense publication
Author: Martin Morgan [aut, cre]
, Tram Nguyen [aut]
, Tyrone Lee [ctb], Nitesh Turaga [ctb], Chan Zuckerberg Initiative DAF CZF2019-002443 [fnd], NIH NCI ITCR U24CA180996 [fnd], NIH NCI IOTN U24CA232979 [fnd], NIH NCI ARTNet U24CA274159 [fnd]
Maintainer: Martin Morgan <mtmorgan.xyz at gmail.com>
citation("AlphaMissenseR")):
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")
BiocManager::install("AlphaMissenseR")
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("AlphaMissenseR")| A. Introduction | HTML | R Script |
| B. AlphaFold Integration | HTML | R Script |
| C. ClinVar Integration | HTML | R Script |
| D. Benchmarking with ProteinGym | HTML | R Script |
| E. Issues & Solutions | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, FunctionalGenomics, GenePrediction, ImmunoOncology, SNP, Software, StructuralPrediction, Transcriptomics, VariantAnnotation |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3.0), dplyr |
| Imports | rjsoncons (>= 1.0.1), DBI, duckdb (>= 1.3.1), rlang, curl, BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats, tools, methods, whisker, ggplot2 |
| System Requirements | |
| URL | https://mtmorgan.github.io/AlphaMissenseR/ |
| Bug Reports | https://github.com/mtmorgan/AlphaMissenseR/issues |
See More
| Suggests | BiocManager, BiocGenerics, S4Vectors, Seqinfo, GenomeInfoDb, GenomicRanges, AnnotationHub, ExperimentHub, ensembldb, httr, tidyr, r3dmol, bio3d, shiny, shiny.gosling, ggdist, colorspace, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | AlphaMissenseR_1.8.0.tar.gz |
| Windows Binary (x86_64) | AlphaMissenseR_1.8.0.zip |
| macOS Binary (big-sur-x86_64) | AlphaMissenseR_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | AlphaMissenseR_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/AlphaMissenseR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AlphaMissenseR |
| Bioc Package Browser | https://code.bioconductor.org/browse/AlphaMissenseR/ |
| Package Short Url | https://bioconductor.org/packages/AlphaMissenseR/ |
| Package Downloads Report | Download Stats |