Package: synapsis 1.11.0
Lucy McNeill
synapsis: An R package to automate the analysis of double-strand break repair during meiosis
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.
Authors:
synapsis_1.11.0.tar.gz
synapsis_1.11.0.zip(r-4.5)synapsis_1.11.0.zip(r-4.4)synapsis_1.11.0.zip(r-4.3)
synapsis_1.11.0.tgz(r-4.4-any)synapsis_1.11.0.tgz(r-4.3-any)
synapsis_1.11.0.tar.gz(r-4.5-noble)synapsis_1.11.0.tar.gz(r-4.4-noble)
synapsis_1.11.0.tgz(r-4.4-emscripten)synapsis_1.11.0.tgz(r-4.3-emscripten)
synapsis.pdf |synapsis.html✨
synapsis/json (API)
NEWS
| # Install 'synapsis' in R: |
| install.packages('synapsis', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:synapsis-1.11.0(bioc 3.20)synapsis-1.10.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:38535ef5ef
Exports:auto_crop_fastcount_fociget_pachytene
Dependencies:abindbase64encBiocGenericsbitopsbslibcachemclidigestEBImageevaluatefastmapfftwtoolsfontawesomefsgluehighrhtmltoolshtmlwidgetsjpegjquerylibjsonliteknitrlatticelifecyclelocfitmemoisemimepngR6rappdirsRCurlrlangrmarkdownsasstifftinytexxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| annotate_foci_counting | annotate_foci_counting |
| annotate_foci_counting_adjusted | annotate_foci_counting_adjusted |
| append_data_frame | append_data_frame |
| auto_crop_fast | auto_crop_fast |
| count_foci | count_foci |
| crop_single_object_fast | crop_single_object_fast |
| get_blobs | get_blobs |
| get_C1 | get_C1 |
| get_coincident_foci | get_coincident_foci |
| get_foci_per_cell | get_foci_per_cell |
| get_overlap_mask | get_overlap_mask |
| get_pachytene | get_pachytene |
| keep_cells | keep_cells |
| make_foci_mask | make_foci_mask |
| make_strand_mask | make_strand_mask |
| remove_XY | remove_XY |