Package: icetea
Type: Package
Title: Integrating Cap Enrichment with Transcript Expression Analysis
Version: 1.31.0
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: GenomeInfoDb, 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: 7.3.2
Config/pak/sysreqs: make libbz2-dev libjpeg-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:48:11 UTC
RemoteUrl: https://github.com/bioc/icetea
RemoteRef: HEAD
RemoteSha: 0b56cf444247b10a5e248703d9d6fd6618d3ff89
NeedsCompilation: no
Packaged: 2026-07-05 13:59:55 UTC; root
Author: Vivek Bhardwaj [aut, cre]
Maintainer: Vivek Bhardwaj <v.bhardwaj@hubrecht.eu>