frenchFISH

DOI: 10.18129/B9.bioc.frenchFISH  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see frenchFISH.

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

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	BiomedicalInformatics, CellBiology, Genetics, HiddenMarkovModel, Preprocessing, Software
Version	1.10.0
In Bioconductor since	BioC 3.11 (R-4.0) (3 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_1.10.0.tar.gz
Windows Binary	frenchFISH_1.10.0.zip (64-bit only)
macOS Binary (x86_64)	frenchFISH_1.10.0.tgz
macOS Binary (arm64)	frenchFISH_1.10.0.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