Package: FISHalyseR 1.41.0

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_1.41.0.tar.gz
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FISHalyseR.pdf |FISHalyseR.html✨
FISHalyseR/json (API)
NEWS

# Install 'FISHalyseR' in R:

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

On BioConductor:FISHalyseR-1.41.0(bioc 3.21)FISHalyseR-1.40.0(bioc 3.20)

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

cellbiology

3.30 score 2 scripts 223 downloads 5 exports 39 dependencies

Last updated 4 months agofrom:51ff6abe2a. Checks:1 OK, 7 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 28 2025
R-4.5-win	WARNING	Jan 28 2025
R-4.5-mac	WARNING	Jan 28 2025
R-4.5-linux	WARNING	Jan 28 2025
R-4.4-win	WARNING	Jan 28 2025
R-4.4-mac	WARNING	Jan 28 2025
R-4.3-win	WARNING	Jan 28 2025
R-4.3-mac	WARNING	Jan 28 2025

Exports:analyseParticles calculateMaxEntropy calculateThreshold computeIlluminationCorrection processFISH

Dependencies:abind base64enc BiocGenerics bitops bslib cachem cli digest EBImage evaluate fastmap fftwtools fontawesome fs generics glue 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::knitron Jan 28 2025.

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