Package: FISHalyseR 1.47.0

Karesh Arunakirinathan

FISHalyseR: FISHalyseR a package for automated FISH quantification

FISHalyseR provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis.

Authors:Karesh Arunakirinathan <[email protected]>, Andreas Heindl <[email protected]>

FISHalyseR_1.47.0.tar.gz
FISHalyseR_1.47.0.zip(r-4.7)FISHalyseR_1.47.0.zip(r-4.6)FISHalyseR_1.47.0.zip(r-4.5)
FISHalyseR_1.47.0.tgz(r-4.6-any)FISHalyseR_1.47.0.tgz(r-4.5-any)
FISHalyseR_1.47.0.tar.gz(r-4.7-any)FISHalyseR_1.47.0.tar.gz(r-4.6-any)
FISHalyseR_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FISHalyseR/json (API)

# Install 'FISHalyseR' in R:

install.packages('FISHalyseR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:FISHalyseR-1.47.0(bioc 3.24)FISHalyseR-1.46.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cellbiology

3.30 score 3 scripts 5 exports 38 dependencies

Last updated from:5e52a472ed. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	152
linux-devel-x86_64	WARNING	152
source / vignettes	OK	178
linux-release-x86_64	WARNING	154
macos-release-arm64	WARNING	118
macos-oldrel-arm64	WARNING	92
windows-devel	WARNING	99
windows-release	WARNING	88
windows-oldrel	WARNING	77
wasm-release	OK	143

Exports:analyseParticles calculateMaxEntropy calculateThreshold computeIlluminationCorrection processFISH

Dependencies:abind base64enc BiocGenerics bitops bslib cachem cli digest EBImage evaluate fastmap fftwtools fontawesome fs generics highr htmltools htmlwidgets jpeg jquerylib jsonlite knitr lattice lifecycle locfit memoise mime png R6 rappdirs RCurl rlang rmarkdown sass tiff tinytex xfun yaml

FISHAlyseR Automated fluorescence in situ hybridisation quantification in R

Rendered fromFISHalyseR.Rnwusingknitr::knitr

Last update: 2015-04-01
Started: 2015-04-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Analyse	analyseParticles
Max Entropy thresholding	calculateMaxEntropy
Compute threshold using Otsu's method	calculateThreshold
Multidimensional Illumination Correction	computeIlluminationCorrection
FISHalyseR - Automated fluorescence in situ hybridisation quantification in R	processFISH