pfamAnalyzeR

DOI: 10.18129/B9.bioc.pfamAnalyzeR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see pfamAnalyzeR.

Identification of domain isotypes in pfam data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	pfamAnalyzeR
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	AlternativeSplicing, Annotation, BiomedicalInformatics, DataImport, FunctionalGenomics, FunctionalPrediction, GenePrediction, Software, SystemsBiology, TranscriptomeVariant
Version	1.0.1
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.3.0), readr, stringr, dplyr
Imports	utils, tibble, magrittr
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/kvittingseerup/pfamAnalyzeR/issues
Depends On Me	IsoformSwitchAnalyzeR
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	pfamAnalyzeR_1.0.1.tar.gz
Windows Binary	pfamAnalyzeR_1.0.1.zip
macOS Binary (x86_64)	pfamAnalyzeR_1.0.1.tgz
macOS Binary (arm64)	pfamAnalyzeR_1.0.1.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