Package: ORFik
Type: Package
Title: Open Reading Frames in Genomics
Version: 1.8.6
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 = "Yamila", family = "Torres Cleuren", email = "yamilatorrescleuren@gmail.com", role = c("ctb", "ths")),
  person(given = "Evind", 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-, RiboSeq-, RNASeq-, TCPseq- and CAGE-data. 
  Focusing on 5' UTRs (leaders), it is generalized in the 
  sense that any transcript region can be analysed. 
  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
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), biomartr, Rsamtools (>=
        1.35.0), BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0),
        SummarizedExperiment (>= 1.14.0), DESeq2 (>= 1.24.0), ggplot2
        (>= 2.2.1), gridExtra (>= 2.3), cowplot (>= 1.0.0), GGally (>=
        1.4.0), methods (>= 3.6.0), R.utils, utils, stats, fst (>=
        0.9.2), tools
RoxygenNote: 7.1.1
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_11
git_last_commit: 3b6321e
git_last_commit_date: 2020-10-05
Date/Publication: 2020-10-08
NeedsCompilation: yes
Packaged: 2020-10-09 03:55:46 UTC; biocbuild
Author: Haakon Tjeldnes [aut, cre, dtc],
  Kornel Labun [aut, cph],
  Katarzyna Chyzynska [ctb, dtc],
  Yamila Torres Cleuren [ctb, ths],
  Evind Valen [ths, fnd]
Maintainer: Haakon Tjeldnes <hauken_heyken@hotmail.com>
Built: R 4.0.2; i386-w64-mingw32; 2020-10-09 15:20:41 UTC; windows
Archs: i386, x64
