Package: ORFik
Type: Package
Title: Open Reading Frames in Genomics
Version: 1.30.2
Encoding: UTF-8
Authors@R: c(
  person(given = "Haakon", family = "Tjeldnes", email = "hauken_heyken@hotmail.com", role = c("aut", "cre", "dtc"), 
   comment = c(ORCID = "0000-0002-2077-747X")),
  person(given = "Kornel", family = "Labun", email = "kornellabun@gmail.com", role = c("aut", "cph")),
  person(given = "Michal", family = "Swirski", email = "michal.swirski@uw.edu.pl", role = c("ctb")),
  person(given = "Katarzyna", family = "Chyzynska", email = "katchyz@gmail.com", role = c("ctb", "dtc")),
  person(given = "Yamila", family = "Torres Cleuren", email = "yamilatorrescleuren@gmail.com", role = c("ctb", "ths")),
  person(given = "Eivind", family = "Valen", email = "eivind.valen@gmail.com", role = c("ths", "fnd")))
Description: R package for analysis of transcript and translation
        features through manipulation of sequence data and NGS data
        like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in
        the sense that any transcript region can be analysed, as the
        name hints to it was made with investigation of ribosomal
        patterns over Open Reading Frames (ORFs) as it's primary use
        case. ORFik is extremely fast through use of C++, data.table
        and GenomicRanges. Package allows to reassign starts of the
        transcripts with the use of CAGE-Seq data, automatic shifting
        of RiboSeq reads, finding of Open Reading Frames for whole
        genomes and much more.
biocViews: ImmunoOncology, Software, Sequencing, RiboSeq, RNASeq,
        FunctionalGenomics, Coverage, Alignment, DataImport
License: MIT + file LICENSE
BugReports: https://github.com/Roleren/ORFik/issues
URL: https://github.com/Roleren/ORFik
Depends: R (>= 4.1.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1),
        GenomicAlignments (>= 1.19.0)
Imports: AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt,
        biomartr (>= 1.0.7), BiocFileCache, BiocGenerics (>= 0.29.1),
        BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0),
        data.table (>= 1.11.8), DESeq2 (>= 1.24.0), fst (>= 0.9.2),
        GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), ggplot2
        (>= 2.2.1), gridExtra (>= 2.3), httr (>= 1.3.0), jsonlite,
        methods (>= 3.6.0), qs2, R.utils, Rcpp (>= 1.0.0), Rsamtools
        (>= 1.35.0), rtracklayer (>= 1.43.0), stats,
        SummarizedExperiment (>= 1.14.0), S4Vectors (>= 0.21.3), tools,
        txdbmaker, utils, XML, xml2 (>= 1.2.0), withr
RoxygenNote: 7.3.3
Suggests: testthat, rmarkdown, knitr, BiocStyle,
        BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDbData
LinkingTo: Rcpp
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-12-19 13:51:11 UTC
RemoteUrl: https://github.com/bioc/ORFik
RemoteRef: RELEASE_3_22
RemoteSha: 201b1e3e65c901129c903708eb8de461eca506f7
NeedsCompilation: yes
Packaged: 2025-12-20 04:04:59 UTC; root
Author: Haakon Tjeldnes [aut, cre, dtc] (ORCID:
    <https://orcid.org/0000-0002-2077-747X>),
  Kornel Labun [aut, cph],
  Michal Swirski [ctb],
  Katarzyna Chyzynska [ctb, dtc],
  Yamila Torres Cleuren [ctb, ths],
  Eivind Valen [ths, fnd]
Maintainer: Haakon Tjeldnes <hauken_heyken@hotmail.com>
Built: R 4.5.2; x86_64-apple-darwin20; 2025-12-20 04:10:07 UTC; unix
