surfaltr

DOI: 10.18129/B9.bioc.surfaltr    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see surfaltr.

Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

Bioconductor version: 3.14

Cell surface proteins form a major fraction of the druggable proteome and can be used for tissue-specific delivery of oligonucleotide/cell-based therapeutics. Alternatively spliced surface protein isoforms have been shown to differ in their subcellular localization and/or their transmembrane (TM) topology. Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM and Phobius. However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, surfaltr. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, surfaltr facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions. Citations for programs mentioned here can be found in the vignette.

Author: Pooja Gangras [aut, cre] , Aditi Merchant [aut]

Maintainer: Pooja Gangras <gangras_pooja at lilly.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("surfaltr")

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("surfaltr")

 

HTML	R Script	surfaltr_vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, DataRepresentation, MultipleComparison, MultipleSequenceAlignment, Software, SplicedAlignment, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.14 (R-4.1) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.0)
Imports	dplyr (>= 1.0.6), biomaRt(>= 2.46.0), protr (>= 1.6-2), seqinr (>= 4.2-5), ggplot2 (>= 3.3.2), utils (>= 2.10.1), stringr (>= 1.4.0), Biostrings(>= 2.58.0), readr (>= 1.4.0), httr (>= 1.4.2), testthat (>= 3.0.0), xml2 (>= 1.3.2), msa(>= 1.22.0), methods (>= 4.0.3)
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Suggests	knitr, rmarkdown, devtools, kableExtra
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Build Report

Package Archives

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

Source Package	surfaltr_1.0.0.tar.gz
Windows Binary	surfaltr_1.0.0.zip
macOS 10.13 (High Sierra)	surfaltr_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/surfaltr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/surfaltr
Package Short Url	https://bioconductor.org/packages/surfaltr/
Package Downloads Report	Download Stats