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frenchFISH

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

Bioconductor version: Release (3.17)

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 1.12.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 years)
License Artistic-2.0
Depends
Imports utils, MCMCpack, NHPoisson
Linking To
Suggests knitr, rmarkdown, testthat
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package frenchFISH_1.12.0.tar.gz
Windows Binary frenchFISH_1.12.0.zip (64-bit only)
macOS Binary (x86_64) frenchFISH_1.12.0.tgz
macOS Binary (arm64) frenchFISH_1.12.0.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/
Package Downloads Report Download Stats