recipe bioconductor-synapsis

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

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/synapsis.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-synapsis/meta.yaml

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.

package bioconductor-synapsis

(downloads) docker_bioconductor-synapsis

versions:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-ebimage:

>=4.44.0,<4.45.0

depends r-base:

>=4.3,<4.4.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-synapsis

and update with::

   mamba update bioconductor-synapsis

To create a new environment, run:

mamba create --name myenvname bioconductor-synapsis

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-synapsis:<tag>

(see `bioconductor-synapsis/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-synapsis/README.html)