pfamAnalyzeR
Identification of domain isotypes in pfam data
Bioconductor version: 3.24 · Package version: 1.13.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pfamAnalyzeR")Details
| Maintainer | Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com> |
| Author | Kristoffer Vitting-Seerup [cre, aut] (ORCID: <https://orcid.org/0000-0002-6450-0608>) |
| License | MIT + file LICENSE |
| Bug Reports | https://github.com/kvittingseerup/pfamAnalyzeR/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | AlternativeSplicing, Annotation, BiomedicalInformatics, DataImport, FunctionalGenomics, FunctionalPrediction, GenePrediction, Software, SystemsBiology, TranscriptomeVariant |
| Package Short Url | https://bioconductor.org/packages/pfamAnalyzeR/ |
Citation
From within R, enter citation("pfamAnalyzeR"):
Kristoffer Vitting-Seerup. pfamAnalyzeR: Identification of domain isotypes in pfam data. doi:10.18129/B9.bioc.pfamAnalyzeR, R package version 1.13.0, https://bioconductor.org/packages/pfamAnalyzeR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | pfamAnalyzeR_1.13.0.tar.gz |
| Windows binary (x86_64) | pfamAnalyzeR_1.13.0.zip |
| macOS binary (arm64) | pfamAnalyzeR_1.13.0.tgz |
| macOS binary (x86_64) | pfamAnalyzeR_1.13.0.tgz |
Reverse dependencies
Depends On Me (1): IsoformSwitchAnalyzeR