Introduction | Preparatory parts of workflow | Installation | Example data description | getQuantileIntensities usage | Use saveImage for quality control and sanity checks | islify support functions | getSizeCutoff | getIntensityCutoff for the antibody (and EGFP) staining(s) | Islify function in its two shapes | Running islify for samples lacking co-expression markers | Running islify including a reference color | Conclusion | Session information
Package: islify 1.5.0
Jakob Theorell
islify: Automatic scoring and classification of cell-based assay images
This software is meant to be used for classification of images of cell-based assays for neuronal surface autoantibody detection or similar techniques. It takes imaging files as input and creates a composite score from these, that for example can be used to classify samples as negative or positive for a certain antibody-specificity. The reason for its name is that I during its creation have thought about the individual picture as an archielago where we with different filters control the water level as well as ground characteristica, thereby finding islands of interest.
Authors:
islify_1.5.0.tar.gz
islify_1.5.0.zip(r-4.7)islify_1.5.0.zip(r-4.6)islify_1.5.0.zip(r-4.5)
islify_1.5.0.tgz(r-4.6-any)islify_1.5.0.tgz(r-4.5-any)
islify_1.5.0.tar.gz(r-4.7-any)islify_1.5.0.tar.gz(r-4.6-any)
islify_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
islify/json (API)
| # Install 'islify' in R: |
| install.packages('islify', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:islify-1.5.0(bioc 3.24)islify-1.4.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwarecellbasedassaysbiomedicalinformaticsfeatureextractionvisualizationpathwaysclassificationopenjdk
Last updated from:3b0b449530. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 186 | ||
| linux-devel-x86_64 | OK | 266 | ||
| source / vignettes | OK | 223 | ||
| linux-release-x86_64 | OK | 256 | ||
| macos-release-arm64 | OK | 205 | ||
| macos-oldrel-arm64 | OK | 128 | ||
| windows-devel | OK | 154 | ||
| windows-release | OK | 157 | ||
| windows-oldrel | OK | 142 | ||
| wasm-release | OK | 150 |
Exports:getIntensityCutoffgetQuantileIntensitiesgetSizeCutoffislifysaveImagezprime
Dependencies:abindautothresholdrbackportsbase64encBiocGenericsbitbit64bitopsbslibcachemcheckmateclicliprcpp11crayondbscandigestdplyrEBImageevaluatefastmapfftwtoolsfontawesomefsgenericsgluehighrhmshtmltoolshtmlwidgetsijtiffjpegjquerylibjsonliteknitrlatticelifecyclelocfitlubridatemagrittrMatrixmemoisemimepillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRBioFormatsRcppRCurlreadrrJavarlangrmarkdownS4Vectorssassstrexstringistringrtibbletidyselecttifftimechangetinytextzdbutf8vctrsvroomwithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Automatic scoring and classification of cell-based assay images | islify-package |
| Identification of an intensity cutoff for a whole experiment | getIntensityCutoff |
| Get information about the quantiles for the intensity values for all colors in an image | getQuantileIntensities |
| Identification of a suitable size cutoff for cells | getSizeCutoff |
| Generation of islands and island derived statistics | islify |
| A few CASPR2-negative cells | negImage |
| A few CASPR2-positive cells | posImage |
| Saving individually coloured png images from raw image input | saveImage |
| Compute the Z'-factor quality score | zprime |
