Package: PICB
Title: piRNA Cluster Builder
Version: 1.2.0
Authors@R: c(person("Pavol", "Genzor",  role = c("aut")),
    person("Aleksandr", "Friman", email="haase-lab-bioinfo@nih.gov",  role = c("aut")),
    person("Daniel", "Stoyko", role = c("aut")),
    person("Parthena", "Konstantinidou", email="haase-lab-bioinfo@nih.gov", role = c("aut")),
    person("Franziska", "Ahrend", email="haase-lab-bioinfo@nih.gov",  role = c("aut", "cre"), comment=c(ORCID = "0009-0004-7464-3444")),
    person("Zuzana", "Loubalova", email="haase-lab-bioinfo@nih.gov",  role = c("aut")), 
    person("Yuejun", "Wang", email="haase-lab-bioinfo@nih.gov",  role = c("aut")),
    person("Hernan", "Lorenzi", email="haase-lab-bioinfo@nih.gov",  role = c("aut")),
    person("Astrid D", "Haase", email="haase-lab-bioinfo@nih.gov",  role = c("aut")))
Description: piRNAs (short for PIWI-interacting RNAs) and their PIWI
        protein partners play a key role in fertility and maintaining
        genome integrity by restricting mobile genetic elements
        (transposons) in germ cells. piRNAs originate from genomic
        regions known as piRNA clusters. The piRNA Cluster Builder
        (PICB) is a versatile toolkit designed to identify genomic
        regions with a high density of piRNAs. It constructs piRNA
        clusters through a stepwise integration of unique and
        multimapping piRNAs and offers wide-ranging parameter settings,
        supported by an optimization function that allows users to test
        different parameter combinations to tailor the analysis to
        their specific piRNA system. The output includes extensive
        metadata columns, enabling researchers to rank clusters and
        extract cluster characteristics.
License: CC0
Encoding: UTF-8
Imports: utils, Seqinfo, GenomicRanges, GenomicAlignments, Biostrings,
        Rsamtools, data.table, IRanges, seqinr, stats, openxlsx, dplyr,
        S4Vectors, methods
Suggests: GenomeInfoDb, knitr, rtracklayer, testthat, BiocStyle,
        prettydoc, BSgenome, BSgenome.Dmelanogaster.UCSC.dm6,
        BiocManager, rmarkdown, ggplot2
VignetteBuilder: knitr
BugReports: https://github.com/HaaseLab/PICB/issues
URL: https://github.com/HaaseLab/PICB
biocViews: Genetics, GenomeAnnotation, Sequencing,
        FunctionalPrediction, Coverage, Transcriptomics
RoxygenNote: 7.3.2
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:34:05 UTC
RemoteUrl: https://github.com/bioc/PICB
RemoteRef: RELEASE_3_22
RemoteSha: b93bc744d90fd7dfc14367feb1fdcd3dd6ce982a
NeedsCompilation: no
Packaged: 2025-11-11 16:39:58 UTC; root
Author: Pavol Genzor [aut],
  Aleksandr Friman [aut],
  Daniel Stoyko [aut],
  Parthena Konstantinidou [aut],
  Franziska Ahrend [aut, cre] (ORCID:
    <https://orcid.org/0009-0004-7464-3444>),
  Zuzana Loubalova [aut],
  Yuejun Wang [aut],
  Hernan Lorenzi [aut],
  Astrid D Haase [aut]
Maintainer: Franziska Ahrend <haase-lab-bioinfo@nih.gov>
Built: R 4.5.2; ; 2025-11-11 16:47:29 UTC; windows
