Package: ORFik
Type: Package
Title: Open Reading Frames in Genomics
Version: 1.6.3
Encoding: UTF-8
Authors@R: c(
  person(given = "Haakon", family = "Tjeldnes", email = "hauken_heyken@hotmail.com", role = c("aut", "cre", "dtc")),
  person(given = "Kornel", family = "Labun", email = "kornellabun@gmail.com", role = c("aut", "cph")),
  person(given = "Katarzyna", family = "Chyzynska", email = "katchyz@gmail.com", role = c("ctb", "dtc")),
  person(given = "Evind", family = "Valen", email = "eivind.valen@gmail.com", role = c("ths", "fnd")) )
Description: Tools for manipulation of sequence-, RiboSeq-, RNASeq- and CageSeq data. 
  ORFik is extremely fast through use of C, data.table and GenomicRanges. 
  Package allows to reassign starts of the transcripts with the use of CageSeq 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
LazyData: TRUE
BugReports: https://github.com/Roleren/ORFik/issues
URL: https://github.com/Roleren/ORFik
Depends: R (>= 3.6.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1),
        GenomicAlignments (>= 1.19.0)
Imports: S4Vectors (>= 0.21.3), GenomeInfoDb (>= 1.15.5),
        GenomicFeatures (>= 1.31.10), AnnotationDbi (>= 1.45.0),
        rtracklayer (>= 1.43.0), Rcpp (>= 1.0.0), data.table (>=
        1.11.8), Biostrings (>= 2.51.1), stats, tools, Rsamtools (>=
        1.35.0), BiocGenerics (>= 0.29.1), SummarizedExperiment (>=
        1.16.0), DESeq2 (>= 1.26.0), ggplot2 (>= 2.2.1), gridExtra (>=
        2.3), GGally (>= 1.4.0), methods (>= 3.6.0)
RoxygenNote: 6.1.1
Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome,
        BSgenome.Hsapiens.UCSC.hg19
LinkingTo: Rcpp
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ORFik
git_branch: RELEASE_3_10
git_last_commit: 1f14a87
git_last_commit_date: 2019-11-19
Date/Publication: 2019-11-19
NeedsCompilation: yes
Packaged: 2019-11-20 04:03:21 UTC; biocbuild
Author: Haakon Tjeldnes [aut, cre, dtc],
  Kornel Labun [aut, cph],
  Katarzyna Chyzynska [ctb, dtc],
  Evind Valen [ths, fnd]
Maintainer: Haakon Tjeldnes <hauken_heyken@hotmail.com>
