Package: surfaltr
Type: Package
Title: Rapid Comparison of Surface Protein Isoform Membrane Topologies
        Through surfaltr
Version: 1.16.0
Authors@R: 
      c(person(given = "Pooja",
           family = "Gangras",
           role = c("aut", "cre"),
           email = "gangras_pooja@lilly.com",
           comment = c(ORCID = "0000-0002-0638-3941")),
      person(given = "Aditi",
           family = "Merchant",  
           email = "aditi.merchant@utexas.edu",
           role = "aut"))
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.
License: MIT + file LICENSE
Encoding: UTF-8
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)
RoxygenNote: 7.1.2
Suggests: knitr, rmarkdown, devtools, kableExtra
VignetteBuilder: knitr
Depends: R (>= 4.0)
NeedsCompilation: no
biocViews: Software, Visualization, DataRepresentation,
        SplicedAlignment, Alignment, MultipleSequenceAlignment,
        MultipleComparison
Packaged: 2025-11-11 17:52:22 UTC; root
Config/testthat/edition: 3
Config/pak/sysreqs: make libicu-dev libpng-dev libxml2-dev libssl-dev
        libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:12:34 UTC
RemoteUrl: https://github.com/bioc/surfaltr
RemoteRef: RELEASE_3_22
RemoteSha: b68ffe3f44bde1e017b640d653c3c9e839409f68
Author: Pooja Gangras [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0638-3941>),
  Aditi Merchant [aut]
Maintainer: Pooja Gangras <gangras_pooja@lilly.com>
Built: R 4.5.2; ; 2025-11-11 18:01:41 UTC; windows
