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Identification of domain isotypes in pfam data

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

pfamAnalyzeR HTML R Script
Reference Manual PDF


biocViews AlternativeSplicing, Annotation, BiomedicalInformatics, DataImport, FunctionalGenomics, FunctionalPrediction, GenePrediction, Software, SystemsBiology, TranscriptomeVariant
Version 1.4.0
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
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Follow Installation instructions to use this package in your R session.

Source Package pfamAnalyzeR_1.4.0.tar.gz
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macOS Binary (x86_64) pfamAnalyzeR_1.4.0.tgz
macOS Binary (arm64) pfamAnalyzeR_1.4.0.tgz
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