Type: Package
Package: TSSr
Title: TSS sequencing data analysis
Version: 0.99.21
Date: 2026-08-21
Authors@R: c(
    person("Zhaolian", "Lu", , "luzhaolian@gmail.com", role = c("aut", "com"),
           comment = c(ORCID = "0000-0001-5002-7007")),
    person("Keenan", "Berry", , "keenan.berry@slu.edu", role = c("aut", "com")),
    person("Zhenbin", "Hu", , "zhenbin.hu@slu.edu", role = c("aut", "ctb")),
    person("Yu", "Zhan", , "yu.zhan@slu.edu", role = c("aut", "ctb")),
    person("Tae-Hyuk (Ted)", "Ahn", , "ted.ahn@slu.edu", role = c("aut", "cph")),
    person("Zhenguo", "Lin", , "zhenguo.lin@slu.edu", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0002-8400-9138")),
    person("National Science Foundation", role = "fnd",
           comment = "NSF 1951332")
  )
Description: TSSr package provides a comprehensive workflow on TSS data
        starts from identification of accurate TSS locations,
        clustering TSSs within small genomic regions corresponding to
        core promoters, and transcriptional activity quantifications,
        as well as specialized downstream analyses including core
        promoter shape, cluster annotation, gene differential
        expression, core promoter shift. TSSr can take multiple formats
        of files as input, such as Binary Sequence Alignment Map (BAM)
        files (single-ended or paired-ended), Browser Extension Data
        (bed) files, BigWig files, ctss files or tss tables. TSSr also
        generates various types of TSS or core promoter track files
        which can be visualized in the UCSC Genome Browser or
        Integrative Genomics Viewer (IGV). TSSr also exports downstream
        analyses result tables and plots.  Multiple cores are supported
        on Linux or Mac platforms.
License: MIT + file LICENSE
URL: https://github.com/Linlab-slu/TSSr
BugReports: https://github.com/Linlab-slu/TSSr/issues
Depends: R (>= 4.5.0)
Imports: BiocGenerics (>= 0.36.1), GenomeInfoDb (>= 1.26.7),
        GenomicFeatures (>= 1.42.3), GenomicRanges (>= 1.42.0), IRanges
        (>= 2.24.1), Rsamtools (>= 2.6.0), cigarillo (>= 0.99.2),
        data.table (>= 1.14.0), dplyr (>= 1.0.7), ggplot2 (>= 3.3.5),
        grDevices (>= 4.0.3), graphics (>= 4.0.3), methods (>= 4.0.3),
        parallel (>= 4.0.3), rtracklayer (>= 1.50.0), stats (>= 4.0.3),
        stringr (>= 1.4.0), txdbmaker (>= 1.0.0), utils (>= 4.0.3)
Suggests: BSgenome.Scerevisiae.UCSC.sacCer3, DESeq2 (>= 1.30.1), Gviz
        (>= 1.34.1), calibrate (>= 1.7.7), ggfortify (>= 0.4.12),
        knitr, pkgdown, rmarkdown, testthat (>= 3.0.0), withr
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: FALSE
NeedsCompilation: no
RoxygenNote: 7.3.3
biocViews: Software, Transcription, Coverage, GeneExpression,
        GeneRegulation, PeakDetection, DataImport, DataRepresentation,
        Transcriptomics, Sequencing, Annotation, GenomeBrowsers,
        Normalization, Preprocessing, Visualization,
        DifferentialExpression, Alignment, Clustering
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: 2026-08-21 20:41:36 UTC
RemoteUrl: https://github.com/bioc/TSSr
RemoteRef: HEAD
RemoteSha: bba29ddb31aa3bcc5c8e1a4276224de759b5b7ea
Packaged: 2026-11-01 14:26:42 UTC; root
Author: Zhaolian Lu [aut, com] (ORCID: <https://orcid.org/0000-0001-5002-7007>),
  Keenan Berry [aut, com],
  Zhenbin Hu [aut, ctb],
  Yu Zhan [aut, ctb],
  Tae-Hyuk (Ted) Ahn [aut, cph],
  Zhenguo Lin [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-8400-9138>),
  National Science Foundation [fnd] (NSF 1951332)
Maintainer: Zhenguo Lin <zhenguo.lin@slu.edu>