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frenchFISH

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


Bioconductor version: Release (3.18)

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.

Author: Adam Berman, Geoff Macintyre

Maintainer: Adam Berman <agb61 at cam.ac.uk>

Citation (from within R, enter citation("frenchFISH")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("frenchFISH")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("frenchFISH")
Correcting FISH probe counts with frenchFISH HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiomedicalInformatics, CellBiology, Genetics, HiddenMarkovModel, Preprocessing, Software
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License Artistic-2.0
Depends
Imports utils, MCMCpack, NHPoisson
System Requirements
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Suggests knitr, rmarkdown, testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package frenchFISH_1.14.0.tar.gz
Windows Binary frenchFISH_1.14.0.zip
macOS Binary (x86_64) frenchFISH_1.14.0.tgz
macOS Binary (arm64) frenchFISH_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/frenchFISH
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/frenchFISH
Bioc Package Browser https://code.bioconductor.org/browse/frenchFISH/
Package Short Url https://bioconductor.org/packages/frenchFISH/
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