frenchFISH

This is the development version of frenchFISH; for the stable release version, see frenchFISH.

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

Bioconductor version: Development (3.24)

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")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, CellBiology, Genetics, HiddenMarkovModel, Preprocessing, Software
Version	1.25.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
License	Artistic-2.0
Depends
Imports	utils, MCMCpack, NHPoisson
System Requirements
URL

Suggests	knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	frenchFISH_1.25.0.tar.gz
Windows Binary (x86_64)	frenchFISH_1.25.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	frenchFISH_1.25.0.tgz
macOS Binary (sonoma-arm64)	frenchFISH_1.25.0.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