DESCRIPTION

Package: icetea
Type: Package
Title: Integrating Cap Enrichment with Transcript Expression Analysis
Version: 1.7.0
Authors@R: person("Vivek", "Bhardwaj", email = "v.bhardwaj@hubrecht.eu", role = c("aut", "cre"))
Description: icetea (Integrating Cap Enrichment with Transcript Expression Analysis)
    provides functions for end-to-end analysis of multiple 5'-profiling methods such as
    CAGE, RAMPAGE and MAPCap, beginning from raw reads to detection of transcription
    start sites using replicates. It also allows performing differential TSS detection
    between group of samples, therefore, integrating the mRNA cap enrichment information
    with transcript expression analysis.
Depends:
    R (>= 4.0)
Imports:
    stats,
    utils,
    methods,
    graphics,
    grDevices,
    ggplot2,
    GenomicFeatures,
    ShortRead,
    BiocParallel,
    Biostrings,
    S4Vectors,
    Rsamtools,
    BiocGenerics,
    IRanges,
    GenomicAlignments,
    GenomicRanges,
    rtracklayer,
    SummarizedExperiment,
    VariantAnnotation,
    limma,
    edgeR,
    csaw,
    DESeq2,
    TxDb.Dmelanogaster.UCSC.dm6.ensGene
Suggests:
    knitr,
    rmarkdown,
    Rsubread (>= 1.29.0),
    testthat
VignetteBuilder: knitr
biocViews: ImmunoOncology, Transcription, GeneExpression, Sequencing,
    RNASeq, Transcriptomics, DifferentialExpression
URL: https://github.com/vivekbhr/icetea
BugReports: https://github.com/vivekbhr/icetea/issues
License: GPL-3 + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.0