frenchFISH

DOI: 10.18129/B9.bioc.frenchFISH    

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

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script Correcting FISH probe counts with frenchFISH
PDF   Reference Manual
Text   NEWS

Details

biocViews BiomedicalInformatics, CellBiology, Genetics, HiddenMarkovModel, Preprocessing, Software
Version 1.2.0
In Bioconductor since BioC 3.11 (R-4.0) (0.5 years)
License Artistic-2.0
Depends
Imports utils, MCMCpack, NHPoisson
LinkingTo
Suggests knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
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_1.2.0.tar.gz
Windows Binary frenchFISH_1.2.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) frenchFISH_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/frenchFISH
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/frenchFISH
Package Short Url https://bioconductor.org/packages/frenchFISH/
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