Package: proActiv
Title: Estimate Promoter Activity from RNA-Seq data
Version: 1.21.0
Authors@R: c(
    person(given = "Deniz",
           family = "Demircioglu",
           role = c("aut"),
           email = "ddemircioglu@gis.a-star.edu.sg",
           comment = c(ORCID = "0000-0001-7857-0407")),
    person(given = "Jonathan",
          family = "Göke",
          role = c("aut"),
          email = "gokej@gis.a-star.edu.sg"),
    person(given = "Joseph",
           family = "Lee",
           role = c("cre"),
           email = "joseph.lee@u.nus.edu"))
Description: Most human genes have multiple promoters that control the
        expression of different isoforms. The use of these alternative
        promoters enables the regulation of isoform expression
        pre-transcriptionally. Alternative promoters have been found to
        be important in a wide number of cell types and diseases.
        proActiv is an R package that enables the analysis of promoters
        from RNA-seq data. proActiv uses aligned reads as input, and
        generates counts and normalized promoter activity estimates for
        each annotated promoter. In particular, proActiv accepts
        junction files from TopHat2 or STAR or BAM files as inputs.
        These estimates can then be used to identify which promoter is
        active, which promoter is inactive, and which promoters change
        their activity across conditions. proActiv also allows
        visualization of promoter activity across conditions.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.0)
RoxygenNote: 7.3.1
Imports: AnnotationDbi, BiocParallel, data.table, dplyr, DESeq2,
        IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments,
        GenomeInfoDb, ggplot2, gplots, graphics, methods, rlang,
        scales, S4Vectors, SummarizedExperiment, stats, tibble,
        txdbmaker
Suggests: GenomeInfoDbData, testthat, rmarkdown, knitr, Rtsne,
        gridExtra
URL: https://github.com/GoekeLab/proActiv
biocViews: RNASeq, GeneExpression, Transcription, AlternativeSplicing,
        GeneRegulation, DifferentialSplicing, FunctionalGenomics,
        Epigenetics, Transcriptomics, Preprocessing
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:02:09 UTC
RemoteUrl: https://github.com/bioc/proActiv
RemoteRef: HEAD
RemoteSha: 806786714823d502835edcf01bd61f57388bab7a
NeedsCompilation: no
Packaged: 2025-10-30 08:35:43 UTC; root
Author: Deniz Demircioglu [aut] (ORCID:
    <https://orcid.org/0000-0001-7857-0407>),
  Jonathan Göke [aut],
  Joseph Lee [cre]
Maintainer: Joseph Lee <joseph.lee@u.nus.edu>
Built: R 4.6.0; ; 2025-10-30 08:38:12 UTC; windows
