idpr
This is the development version of idpr; for the stable release version, see idpr.
Profiling and Analyzing Intrinsically Disordered Proteins in R
Bioconductor version: Development (3.24)
‘idpr’ aims to integrate tools for the computational analysis of intrinsically disordered proteins (IDPs) within R. This package is used to identify known characteristics of IDPs for a sequence of interest with easily reported and dynamic results. Additionally, this package includes tools for IDP-based sequence analysis to be used in conjunction with other R packages. Described in McFadden WM & Yanowitz JL (2022). "idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R." PloS one, 17(4), e0266929.
Author: William M. McFadden [cre, aut], Judith L. Yanowitz [aut, fnd], Michael Buszczak [ctb, fnd]
Maintainer: William M. McFadden <wmm27 at pitt.edu>
citation("idpr")):
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("idpr")
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("idpr")| Charge and Hydropathy Vignette | HTML | R Script |
| Disordered Matrices Vignette | HTML | R Script |
| idpr Package Overview Vignette | HTML | R Script |
| IUPred Vignette | HTML | R Script |
| Sequence Map Vignette | HTML | R Script |
| Structural Tendency Vignette | HTML | R Script |
| Reference Manual |
Details
| biocViews | CellBiology, Proteomics, Software, StructuralPrediction |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | LGPL (>= 3) |
| Depends | R (>= 4.1.0) |
| Imports | ggplot2 (>= 3.3.0), magrittr (>= 1.5), dplyr (>= 0.8.5), plyr (>= 1.8.6), jsonlite (>= 1.6.1), rlang (>= 0.4.6), Biostrings(>= 2.56.0), methods (>= 4.0.0) |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/wmm27/idpr/issues |
See More
| Suggests | knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr |
| 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 | idpr_1.23.0.tar.gz |
| Windows Binary (x86_64) | idpr_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | idpr_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | idpr_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/idpr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/idpr |
| Bioc Package Browser | https://code.bioconductor.org/browse/idpr/ |
| Package Short Url | https://bioconductor.org/packages/idpr/ |
| Package Downloads Report | Download Stats |