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pfamAnalyzeR

Identification of domain isotypes in pfam data


Bioconductor version: Release (3.18)

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 1.2.0
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
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Build Report Build Report

Package Archives

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

Source Package pfamAnalyzeR_1.2.0.tar.gz
Windows Binary pfamAnalyzeR_1.2.0.zip
macOS Binary (x86_64) pfamAnalyzeR_1.2.0.tgz
macOS Binary (arm64) pfamAnalyzeR_1.2.0.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