Package: surfaltr
Type: Package
Title: Rapid Comparison of Surface Protein Isoform Membrane Topologies
        Through surfaltr
Version: 1.15.0
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: 2025-06-05 02:28:00 UTC; biocbuild
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/surfaltr
git_branch: devel
git_last_commit: 6a27561
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
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 4.5.0; ; 2025-06-05 14:09:38 UTC; windows
