BIOCONDUCTOR . ORG {
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Title:
Bioconductor - surfaltr
Description:
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.
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Keywords {🔍}
package, bioconductor, surfaltr, version, packages, surface, protein, topologies, release, source, isoform, isoforms, gangras, enter, install, license, binary, learn, developers, started, software, rapid, comparison, membrane, proteins, alternatively, spliced, topology, methods, tmhmm, phobius, pairs, alignment, pooja, aut, merchant, httpsbioconductororgpackagessurfaltr, installation, start, documentation, system, text, details, bioc, url, macos, surfaltrtgz, repository, git, clone,
Topics {✒️}
org/packages/surfaltr source repository joint galaxy/bioconductor conference oligonucleotide/cell-based therapeutics bioconductor release tgz source repository source package org/packages/surfaltr release //code bioconductor support site pairs inputted isoforms protein alignment functions tissue-specific delivery streamline batch processing customizable graphical output script reference manual gz windows binary zip macos binary tgz macos binary pooja gangras [aut git clone https package installed details biocviews package version 1 surface proteins alternatively spliced started install packages package tm topologies visualizing topologies surfaltr facilitates //bioconductor bioconductor surfaltr doi registration open rapid comparison major fraction druggable proteome subcellular localization remain difficult bioinformatic approaches ranking metrics programs mentioned cre] orcid quietly = true older versions pdf news developer access org
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