Type: Package
Package: TSSr
Title: TSS sequencing data analysis
Version: 0.99.11
Date: 2026-05-07
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 (>= 4.6.0)
Imports: BiocGenerics (>= 0.36.1), DESeq2 (>= 1.30.1), GenomeInfoDb (>=
        1.26.7), GenomicFeatures (>= 1.42.3), GenomicRanges (>=
        1.42.0), Gviz (>= 1.34.1), IRanges (>= 2.24.1), Rsamtools (>=
        2.6.0), calibrate (>= 1.7.7), data.table (>= 1.14.0), dplyr (>=
        1.0.7), ggfortify (>= 0.4.12), 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, 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
Packaged: 2026-05-07 20:26:29 UTC; pkgbuild
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>
