surfaltr
Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr
Bioconductor version: Release (3.17)
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>
citation("surfaltr")):
Installation
To install this package, start R (version "4.3") 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")| surfaltr_vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, DataRepresentation, MultipleComparison, MultipleSequenceAlignment, Software, SplicedAlignment, Visualization |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2 years) |
| 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) |
| Linking To | |
| Suggests | knitr, rmarkdown, devtools, kableExtra |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | surfaltr_1.6.0.tar.gz |
| Windows Binary | surfaltr_1.6.0.zip |
| macOS Binary (x86_64) | surfaltr_1.6.0.tgz |
| macOS Binary (arm64) | surfaltr_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/surfaltr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/surfaltr |
| Bioc Package Browser | https://code.bioconductor.org/browse/surfaltr/ |
| Package Short Url | https://bioconductor.org/packages/surfaltr/ |
| Package Downloads Report | Download Stats |