mitoODE

DOI: 10.18129/B9.bioc.mitoODE    

This is the development version of mitoODE; to use it, please install the devel version of Bioconductor.

Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"

Bioconductor version: Development (3.10)

The package contains the methods to fit a cell-cycle model on cell count data and the code to reproduce the results shown in our paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" by Pau, G., Walter, T., Neumann, B., Heriche, J.-K., Ellenberg, J., & Huber, W., BMC Bioinformatics (2013), 14(1), 308. doi:10.1186/1471-2105-14-308

Author: Gregoire Pau

Maintainer: Gregoire Pau <pau.gregoire at gene.com>

Citation (from within R, enter citation("mitoODE")):

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("mitoODE")

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("mitoODE")

 

PDF R Script mitoODE
PDF   Reference Manual
Text   NEWS

Details

biocViews CellBasedAssays, ExperimentData, ImmunoOncology, Preprocessing, Software, TimeCourse
Version 1.23.0
In Bioconductor since BioC 2.13 (R-3.0) (6 years)
License LGPL
Depends R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata, KernSmooth
Imports
LinkingTo
Suggests
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 mitoODE_1.23.0.tar.gz
Windows Binary mitoODE_1.23.0.zip
Mac OS X 10.11 (El Capitan) mitoODE_1.23.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/mitoODE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/mitoODE
Package Short Url http://bioconductor.org/packages/mitoODE/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: