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>

Citation (from within R, enter citation("pfamAnalyzeR")):

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")
pfamAnalyzeR HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

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) (1 year)
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_1.0.1.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
Old Source Packages for BioC 3.17 Source Archive