{ "_id": "6a1af3831d7bb097a09f8527", "Package": "surfaltr", "Type": "Package", "Title": "Rapid Comparison of Surface Protein Isoform Membrane Topologies\nThrough surfaltr", "Version": "1.19.0", "Authors@R": "c(person(given = \"Pooja\",\nfamily = \"Gangras\",\nrole = c(\"aut\", \"cre\"),\nemail = \"gangras_pooja@lilly.com\",\ncomment = c(ORCID = \"0000-0002-0638-3941\")),\nperson(given = \"Aditi\",\nfamily = \"Merchant\",\nemail = \"aditi.merchant@utexas.edu\",\nrole = \"aut\"))", "Description": "Cell surface proteins form a major fraction of the\ndruggable proteome and can be used for tissue-specific delivery\nof oligonucleotide/cell-based therapeutics. Alternatively\nspliced surface protein isoforms have been shown to differ in\ntheir subcellular localization and/or their transmembrane (TM)\ntopology. Surface proteins are hydrophobic and remain difficult\nto study thereby necessitating the use of TM topology\nprediction methods such as TMHMM and Phobius. However, there\nexists a need for bioinformatic approaches to streamline batch\nprocessing of isoforms for comparing and visualizing\ntopologies. To address this gap, we have developed an R\npackage, surfaltr. It pairs inputted isoforms, either known\nalternatively spliced or novel, with their APPRIS annotated\nprincipal counterparts, predicts their TM topologies using\nTMHMM or Phobius, and generates a customizable graphical\noutput. Further, surfaltr facilitates the prioritization of\nbiologically diverse isoform pairs through the incorporation of\nthree different ranking metrics and through protein alignment\nfunctions. Citations for programs mentioned here can be found\nin the vignette.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.1.2", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "biocViews": "Software, Visualization, DataRepresentation,\nSplicedAlignment, Alignment, MultipleSequenceAlignment,\nMultipleComparison", "Packaged": { "Date": "2026-05-30 09:45:01 UTC", "User": "root" }, "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:57:05 UTC", "RemoteUrl": "https://github.com/bioc/surfaltr", "RemoteRef": "HEAD", "RemoteSha": "1cadef7389a5b76ad8c495925aebbf1c843d20e6", "Author": "Pooja Gangras [aut, cre] (ORCID:\n),\nAditi Merchant [aut]", "Maintainer": "Pooja Gangras ", "MD5sum": "926537587a395165d72f0cfd68f9c5c1", "_user": "bioc", "_type": "src", "_file": "surfaltr_1.19.0.tar.gz", 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"hpa_mouse_genes", "title": "SurfaltR Gene Name and Transcript ID Test Data- Highly Expressed Mouse Alternative Transcripts", "topics": [ "hpa_mouse_genes" ] }, { "page": "merge_trans", "title": "Associate Inputted Transcripts with Corresponding Primary Transcripts", "topics": [ "merge_trans" ] }, { "page": "plot_isoforms", "title": "Create a plot showing where each amino acid is located within the cell for each primary transcript compared to each alternative transcript", "topics": [ "plot_isoforms" ] }, { "page": "process_tmhmm", "title": "Create a data frame with the membrane locations of each amino acid in a sequence", "topics": [ "process_tmhmm" ] }, { "page": "rank_prts", "title": "Rank the surface proteins by differences in principal and alternative isoforms", "topics": [ "rank_prts" ] }, { "page": "run_phobius", "title": "Create a data frame with the membrane locations of each amino acid in a protein using Phobius", "topics": [ "run_phobius" ] }, { "page": "split_fasta", "title": "Split a fasta formatted file.", "topics": [ "split_fasta" ] }, { "page": "test_surfaltr", "title": "Test the functionality of surfaltr", "topics": [ "test_surfaltr" ] }, { "page": "tmhmm_fix_path", "title": "Retrieve Data from TMHMM and Fix Functionality of TMHMM R Package", "topics": [ "tmhmm_fix_path" ] } ], "_readme": "https://github.com/bioc/surfaltr/raw/HEAD/README.md", "_rundeps": [ "ade4", "AnnotationDbi", "askpass", "Biobase", "BiocFileCache", "BiocGenerics", "biomaRt", "Biostrings", "bit", "bit64", "blob", "brio", "cachem", "callr", "cli", "clipr", "cpp11", "crayon", "curl", "DBI", "dbplyr", "desc", "diffobj", "dplyr", "evaluate", "farver", "fastmap", "filelock", "fs", "generics", "ggplot2", "glue", "gtable", "hms", "httr", "httr2", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "memoise", "mime", "msa", "nlme", "openssl", "pillar", "pixmap", "pkgbuild", "pkgconfig", "pkgload", "png", "praise", "prettyunits", 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pipeline and quick start", "How to get help for surfaltr", "Input data", "Obtaining and Formatting Input Data", "Why filter genes known to encode surface proteins?", "Gene name and transcript ID’s input (Input type 1)", "Gene name and amino acid sequence input (Input type 2)", "About the example datasets", "Rapid Plotting of Paired Isoforms", "From known Ensembl Transcript Models (Input type 1)", "From Amino Acid Sequence Input (Input type 2)", "Isoform Pairing of Input Data and FASTA File Generation", "Output 1: Paired Isoforms", "Output 2: FASTA File", "Determine TM topology", "When to Use TMHMM", "Using Phobius", "Interpreting Results from Both Phobius and TMHMM", "Ranking and Plotting of Isoform Pairs", "Ranking criteria", "Ranked by Length", "Ranked by Number of TM Domains", "Ranked by Combo Metric", "Choosing and Formatting Isoform Pairs to Display", "Plot Interpretation", "Multiple Sequence Alignment for Genes of Interest", "From Isoform Pairs from a Single Organism", "From Isoform Pairs from Multiple Organisms", "Interpreting Alignment Results and Isoform Pair Plots", "References" ], "created": "2021-07-30 13:52:48", "modified": "2022-05-02 19:51:59", "commits": 9 } ], "_score": 4, "_indexed": true, "_nocasepkg": "surfaltr", "_universes": [ "bioc", "pgangras" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-05-30T10:17:34.000Z", "distro": "noble", "commit": "1cadef7389a5b76ad8c495925aebbf1c843d20e6", "fileid": "afdbe437a640b7b0b11a8efa72ca827ad9b33aaa984aa3fc0cbc2bc83523627f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676745372" }, { "r": "4.6.0", "os": "linux", "version": "1.19.0", "date": "2026-05-30T10:17:50.000Z", "distro": "noble", "commit": "1cadef7389a5b76ad8c495925aebbf1c843d20e6", "fileid": "1b19c305c04997415233a217d79072f5fdf13e8a4e743d1dd6ad04b04b9dff77", "status": "success", "check": "OK", "buildurl": 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