frenchFISH
This package is for version 3.12 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: 3.12
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("frenchFISH")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, CellBiology, Genetics, HiddenMarkovModel, Preprocessing, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | Artistic-2.0 |
| Depends | |
| Imports | utils, MCMCpack, NHPoisson |
| System Requirements | |
| URL |
See More
| 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_1.2.0.tar.gz |
| Windows Binary | frenchFISH_1.2.0.zip |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/frenchFISH/ |
| Package Short Url | https://bioconductor.org/packages/frenchFISH/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |