pfamAnalyzeR
This is the development version of pfamAnalyzeR; for the stable release version, see pfamAnalyzeR.
Identification of domain isotypes in pfam data
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Kristoffer Vitting-Seerup <k.vitting.seerup at gmail.com>
citation("pfamAnalyzeR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, Annotation, BiomedicalInformatics, DataImport, FunctionalGenomics, FunctionalPrediction, GenePrediction, Software, SystemsBiology, TranscriptomeVariant |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| 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_1.7.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |