DESCRIPTION

Package: riboWaltz
Type: Package
Title: Optimization of ribosome P-site positioning in ribosome profiling data
Version: 2.0
Authors@R: c(
    person("Fabio", "Lauria", email = "fabio.lauria@gmail.com", role = c("aut", "cre")),
    person("Toma", "Tebaldi", email = "toma.tebaldi@gmail.com", role = "aut"),
    person("Gabriella", "Viero", email = "gabriella.viero@cnr.it", role = "aut"))
Description: riboWaltz is an R package designed for the analysis of
    ribosome profiling (RiboSeq) data aimed at the identification of the
    P-site offset. The P-site offset (PO) is specified by the localization of
    the P-site of ribosomes within the fragments of the RNA (reads) resulting
    from RiboSeq assays. It is defined as the distance of the P-site from the
    two ends of the reads. Determining the PO is a crucial step for a variety of
    RiboSeq-based analyses such as verify the so-called 3-nt periodicity of
    ribosomes along the coding sequence, derive translation initiation and
    elongation rates and reveal new translational events in unannotated open
    reading frames and ncRNAs. riboWaltz performs accurate computation of the
    PO for all the lengths of reads from single or multiple samples, taking
    advantage from an original two-step algorithm. Moreover, riboWaltz
    provides the user a variety of graphical representations, laying
    the groundwork for further positional analyses and new biological
    discoveries.
License: MIT + file LICENSE
LazyData: TRUE
Depends:
    R (>= 3.3.0)
Imports:
	Biostrings (>= 2.46.0),
	data.table (>= 1.10.4.3),
	GenomicAlignments (>= 1.14.1),
	GenomicFeatures (>= 1.24.5),
	GenomicRanges (>= 1.24.3),
	ggplot2 (>= 2.2.1),
	ggrepel (>= 0.6.5),
	IRanges (>= 2.12.0)
biocViews:
RoxygenNote: 7.1.1
Roxygen: list(markdown = TRUE)
Encoding: UTF-8
Suggests:
    knitr,
    rmarkdown
VignetteBuilder: knitr