pfamAnalyzeR
This is the released version of pfamAnalyzeR; for the devel version, see pfamAnalyzeR.
Identification of domain isotypes in pfam data
Bioconductor version: Release (3.23)
Protein domains is one of the most import annoation of proteins we have with the Pfam database/tool being (by far) the most used tool. This R package enables the user to read the pfam prediction from both webserver and stand-alone runs into R. We have recently shown most human protein domains exist as multiple distinct variants termed domain isotypes. Different domain isotypes are used in a cell, tissue, and disease-specific manner. Accordingly, we find that domain isotypes, compared to each other, modulate, or abolish the functionality of a protein domain. This R package enables the identification and classification of such domain isotypes from Pfam data.
Author: Kristoffer Vitting-Seerup [cre, aut]
Maintainer: Kristoffer Vitting-Seerup <k.vitting.seerup at gmail.com>
citation("pfamAnalyzeR")):
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("pfamAnalyzeR")
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("pfamAnalyzeR")| pfamAnalyzeR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, Annotation, BiomedicalInformatics, DataImport, FunctionalGenomics, FunctionalPrediction, GenePrediction, Software, SystemsBiology, TranscriptomeVariant |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3.0), readr, stringr, dplyr |
| Imports | utils, tibble, magrittr |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/kvittingseerup/pfamAnalyzeR/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | IsoformSwitchAnalyzeR |
| 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 | pfamAnalyzeR_1.12.0.tar.gz |
| Windows Binary (x86_64) | pfamAnalyzeR_1.12.0.zip |
| macOS Binary (big-sur-x86_64) | pfamAnalyzeR_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | pfamAnalyzeR_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/pfamAnalyzeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pfamAnalyzeR |
| Bioc Package Browser | https://code.bioconductor.org/browse/pfamAnalyzeR/ |
| Package Short Url | https://bioconductor.org/packages/pfamAnalyzeR/ |
| Package Downloads Report | Download Stats |