procoil
This is the development version of procoil; for the stable release version, see procoil.
Prediction of Oligomerization of Coiled Coil Proteins
Bioconductor version: Development (3.24)
The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps.
Author: Ulrich Bodenhofer [aut, cre]
Maintainer: Ulrich Bodenhofer <ulrich at bodenhofer.com>
citation("procoil")):
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("procoil")
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("procoil")| PrOCoil - A Web Service and an R Package for Predicting the Oligomerization of Coiled-Coil Proteins | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Proteomics, Software, SupportVectorMachine |
| Version | 2.41.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (15.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.3.0), kebabs |
| Imports | methods, stats, graphics, S4Vectors, Biostrings, utils |
| System Requirements | |
| URL | https://github.com/UBod/procoil |
See More
| Suggests | knitr |
| 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 | procoil_2.41.0.tar.gz |
| Windows Binary (x86_64) | procoil_2.41.0.zip |
| macOS Binary (big-sur-x86_64) | procoil_2.41.0.tgz |
| macOS Binary (sonoma-arm64) | procoil_2.41.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/procoil |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/procoil |
| Bioc Package Browser | https://code.bioconductor.org/browse/procoil/ |
| Package Short Url | https://bioconductor.org/packages/procoil/ |
| Package Downloads Report | Download Stats |