synapsis

DOI: 10.18129/B9.bioc.synapsis  

An R package to automate the analysis of double-strand break repair during meiosis

Bioconductor version: Release (3.16)

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.

Author: Lucy McNeill [aut, cre, cph] , Wayne Crismani [rev, ctb]

Maintainer: Lucy McNeill <luc.mcneill at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("synapsis")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("synapsis")

 

HTML	R Script	Using-synapsis
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	SingleCell, Software
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.1)
Imports	EBImage, stats, utils, graphics
LinkingTo
Suggests	knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	synapsis_1.4.0.tar.gz
Windows Binary	synapsis_1.4.0.zip
macOS Binary (x86_64)	synapsis_1.4.0.tgz
macOS Binary (arm64)	synapsis_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/synapsis
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/synapsis
Bioc Package Browser	https://code.bioconductor.org/browse/synapsis/
Package Short Url	https://bioconductor.org/packages/synapsis/
Package Downloads Report	Download Stats