Overview | Getting started | Detailed Example | Choosing ROIs | Calculating Correlation Statistics | Selecting a multiple regions in an image | Analyzing a collection of images at once | Reproducing the shiny app output | Description of the co-localization statistics | PCC | MOC | Colocalization Benchmark Source | Acknowledgement
Package: colocr 0.1.1
Mahmoud Ahmed
colocr: Conduct Co-Localization Analysis of Fluorescence Microscopy Images
Automate the co-localization analysis of fluorescence microscopy images. Selecting regions of interest, extract pixel intensities from the image channels and calculate different co-localization statistics. The methods implemented in this package are based on Dunn et al. (2011) <doi:10.1152/ajpcell.00462.2010>.
Authors:
colocr_0.1.1.tar.gz
colocr_0.1.1.zip(r-4.7)colocr_0.1.1.zip(r-4.6)colocr_0.1.1.zip(r-4.5)
colocr_0.1.1.tgz(r-4.6-any)colocr_0.1.1.tgz(r-4.5-any)
colocr_0.1.1.tar.gz(r-4.7-any)colocr_0.1.1.tar.gz(r-4.6-any)
colocr_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
colocr/json (API)
| # Install 'colocr' in R: |
| install.packages('colocr', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) |
Reviews:rOpenSci Software Review #243
Bug tracker:https://github.com/ropensci/colocr/issues
Pkgdown/docs site:https://docs.ropensci.org
Last updated from:9b7bd6ef54 (on master). Checks:7 NOTE, 3 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 180 | ||
| pkgdown docs | OK | 216 | ||
| source / vignettes | OK | 257 | ||
| linux-release-x86_64 | NOTE | 186 | ||
| macos-release-arm64 | NOTE | 136 | ||
| macos-oldrel-arm64 | NOTE | 111 | ||
| windows-devel | NOTE | 148 | ||
| windows-release | NOTE | 147 | ||
| windows-oldrel | NOTE | 165 | ||
| wasm-release | OK | 161 |
Exports:.intensity_get.labels_add.manders.pearson%>%colocr_appimage_loadroi_checkroi_selectroi_showroi_test
Dependencies:base64encbmpbslibcachemclicommonmarkcpp11curldigestdownloaderfarverfastmapfontawesomefsgluehtmltoolshttpuvigraphimagerjpegjquerylibjsonlitelabelinglaterlatticelifecyclemagickmagrittrMatrixmemoisemimeotelpkgconfigpngpromisespurrrR6rappdirsRColorBrewerRcppreadbitmaprlangsassscalesshinysourcetoolsstringistringrtiffvctrsviridisLitewithrxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get pixel intensities | .intensity_get |
| Label regions of interest | .labels_add |
| Calculate Marnders Overlap Coefficient | .manders |
| Calculate Pearson's Correlation Coefficient | .pearson |
| 'colocr': Conduct Co-localization Analysis of Microscopy Images. | colocr-package colocr |
| Run the shiny App | colocr_app |
| Load images from files | image_load |
| Show pixel intensities | roi_check |
| Select regions of interest | roi_select |
| Show the selected regions of interest | roi_show |
| Test Co-localization | roi_test |
