- recipe bioconductor-synapsis
An R package to automate the analysis of double-strand break repair during meiosis
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/synapsis.html
- License:
MIT + file LICENSE
- Recipe:
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¶
-
- Versions:
1.4.0-0
,1.0.0-0
- Depends:
bioconductor-ebimage
>=4.40.0,<4.41.0
r-base
>=4.2,<4.3.0a0
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-synapsis
and update with:
conda update bioconductor-synapsis
or 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 badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-synapsis/README.html)