Package: ribosomeProfilingQC
Type: Package
Title: Ribosome Profiling Quality Control
Version: 1.13.2
Authors@R: c(person(given="Jianhong", family="Ou", email="", 
        role=c("aut", "cre"), comment=c(ORCID="0000-0002-8652-2488")),
        person(given="Mariah", family="Hoye", email="",
Description: Ribo-Seq (also named ribosome profiling or footprinting) 
        measures translatome (unlike RNA-Seq, which sequences the transcriptome)
        by direct quantification of the ribosome-protected fragments (RPFs). 
        This package provides the tools for quality assessment of ribosome 
        profiling. In addition, it can preprocess Ribo-Seq data for subsequent
        differential analysis. 
License: GPL (>=3) + file LICENSE
Encoding: UTF-8
LazyData: true
biocViews: RiboSeq, Sequencing, GeneRegulation, QualityControl, 
           Visualization, Coverage
VignetteBuilder: knitr
RoxygenNote: 7.2.3
Depends: R (>= 4.0), GenomicRanges
Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq,
         GenomicAlignments, GenomicFeatures, GenomeInfoDb,
         IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread,
         S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils,
         cluster, stats, graphics, grid
Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, 
          edgeR, limma, testthat, rmarkdown