Package: frenchFISH 1.19.0

Adam Berman

frenchFISH: Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections

FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting.

Authors:Adam Berman, Geoff Macintyre

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frenchFISH.pdf |frenchFISH.html✨
frenchFISH/json (API)
NEWS

# Install 'frenchFISH' in R:
install.packages('frenchFISH', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:frenchFISH-1.17.0(bioc 3.20)frenchFISH-1.16.0(bioc 3.19)

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

softwarebiomedicalinformaticscellbiologygeneticshiddenmarkovmodelpreprocessing

4.00 score 3 scripts 110 downloads 3 exports 64 dependencies

Last updated 20 days agofrom:4b9c985a9e. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 30 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macOKOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 30 2024

Exports:convertFishalyserCsvToCountMatrixgetAutomaticCountsEstimatesgetManualCountsEstimates

Dependencies:abindbackportsbootbroomcarcarDataclicodacolorspacecowplotcpp11DerivdoBydplyrfansifarverFormulagenericsggplot2gluegtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmcmcMCMCpackmgcvmicrobenchmarkminqamodelrmunsellNHPoissonnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpurrrquantregR6RColorBrewerRcppRcppEigenrlangscalesSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr

Correcting FISH probe counts with frenchFISH

Adam Berman

Rendered fromfrenchFISH.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2020-02-17
Started: 2020-02-05

Readme and manuals

Help Manual

Help pageTopics
Helper function to check if all values in the input count matrix are either NA, NaN, or non-negative integersareAllNonnegativeIntegers
Helper function to check the arguments input to getAutomaticCountsEstimatescheckAutomaticCountsEstimatesArguments
Helper function to check the arguments input to getManualCountsEstimatescheckManualCountsEstimatesArguments
Function to convert CSV output of the FISHalyseR automatic FISH splot counting software to a count matrix suitable for input to frenchFISH's getAutomaticCountsEstimatesconvertFishalyserCsvToCountMatrix
Helper function to convert spot counts and nuclear area measurements into continuous events for Poisson point estimationgeneratePPdat
FrenchFISH function for generating Poisson point estimates of spot counts from spot counts which have been automatically generated.getAutomaticCountsEstimates
Helper function to get the average volume of nucleus sampled given the nucleus radius and section heightgetAverageVolumeFrac
FrenchFISH function for generating volume adjusted spot counts from spots which have been manually counted (uses a Markov chain Monte Carlo method).getManualCountsEstimates
Helper function to get the maximum possible volume of nucleus sampled given the nucleus radius and section heightgetMaxVolumeFrac
Helper function that returns the minimum possible volume of nucleus sampled given the nucleus radius and section heightgetMinVolumeFrac
Helper function that returns the fraction of the nucleus sampled for a specified distance from the midpointgetVsegFrac