Package: synapsis
Type: Package
Title: An R package to automate the analysis of double-strand break
        repair during meiosis
Version: 1.16.0
Authors@R: 
    c(person(given = "Lucy",
             family = "McNeill",
             role = c("aut", "cre", "cph"),
             email = "luc.mcneill@gmail.com",
             comment = c(ORCID = "0000-0003-1752-4882")),
      person(given = "Wayne",
             family = "Crismani",
             role = c("rev", "ctb"),
             comment = c(ORCID = "0000-0003-0143-8293")))
Description: Synapsis is a Bioconductor software package for automated
        (unbiased and reproducible) analysis of meiotic
        immunofluorescence datasets. The primary functions of the
        software can i) identify cells in meiotic prophase that are
        labelled by a synaptonemal complex axis or central element
        protein, ii) isolate individual synaptonemal complexes and
        measure their physical length, iii) quantify foci and
        co-localise them with synaptonemal complexes, iv) measure
        interference between synaptonemal complex-associated foci. The
        software has applications that extend to multiple species and
        to the analysis of other proteins that label meiotic prophase
        chromosomes. The software converts meiotic immunofluorescence
        images into R data frames that are compatible with machine
        learning methods. Given a set of microscopy images of meiotic
        spread slides, synapsis crops images around individual single
        cells, counts colocalising foci on strands on a per cell basis,
        and measures the distance between foci on any given strand.
biocViews: Software, SingleCell
Depends: R (>= 4.1)
Imports: EBImage, stats, utils, graphics
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse,
        BiocStyle
Config/testthat/edition: 3
Config/pak/sysreqs: libfftw3-dev make libjpeg-dev libpng-dev
        libtiff-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:13:22 UTC
RemoteUrl: https://github.com/bioc/synapsis
RemoteRef: RELEASE_3_22
RemoteSha: 184fc99b19f2ae0d800416b8bd3572e50e9c85dc
NeedsCompilation: no
Packaged: 2026-02-03 08:26:56 UTC; root
Author: Lucy McNeill [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-1752-4882>),
  Wayne Crismani [rev, ctb] (ORCID:
    <https://orcid.org/0000-0003-0143-8293>)
Maintainer: Lucy McNeill <luc.mcneill@gmail.com>
Built: R 4.5.2; ; 2026-02-03 08:28:13 UTC; windows
