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.

Author
Karesh Arunakirinathan <akaresh88@gmail.com>, Andreas Heindl <andreas.heindl@icr.ac.uk>
Date of publication
None
Maintainer
Karesh Arunakirinathan <akaresh88@gmail.com>, Andreas Heindl <andreas.heindl@icr.ac.uk>
License
Artistic-2.0
Version
1.8.0

View on Bioconductor

Man pages

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

Files in this package

FISHalyseR/DESCRIPTION
FISHalyseR/NAMESPACE
FISHalyseR/NEWS
FISHalyseR/R
FISHalyseR/R/CreateVectors.R
FISHalyseR/R/FISHalyseR-Ex.R
FISHalyseR/R/GetDistances.R
FISHalyseR/R/GetStain.R
FISHalyseR/R/analyseParticles.R
FISHalyseR/R/calculateMaxEntropy.R
FISHalyseR/R/calculateThreshold.R
FISHalyseR/R/computeIlluminationCorrection.R
FISHalyseR/R/processFISH.R
FISHalyseR/build
FISHalyseR/build/vignette.rds
FISHalyseR/inst
FISHalyseR/inst/doc
FISHalyseR/inst/doc/FISHalyseR.R
FISHalyseR/inst/doc/FISHalyseR.Rnw
FISHalyseR/inst/doc/FISHalyseR.pdf
FISHalyseR/inst/extdata
FISHalyseR/inst/extdata/SampleFISH.jpg
FISHalyseR/inst/extdata/SampleFISH_B.jpg
FISHalyseR/inst/extdata/SampleFISH_G.jpg
FISHalyseR/inst/extdata/SampleFISH_R.jpg
FISHalyseR/inst/extdata/SampleFISHgray.jpg
FISHalyseR/inst/extdata/SampleFISHillu.jpg
FISHalyseR/man
FISHalyseR/man/analyseParticles.Rd
FISHalyseR/man/calculateMaxEntropy.Rd
FISHalyseR/man/calculateThreshold.Rd
FISHalyseR/man/computeIlluminationCorrection.Rd
FISHalyseR/man/processFISH.Rd
FISHalyseR/vignettes
FISHalyseR/vignettes/FISHalyseR.Rnw