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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("mitoODE")
In most cases, you don't need to download the package archive at all.
mitoODE
Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"
Bioconductor version: 2.14
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 and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("mitoODE")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("mitoODE")
| R Script | mitoODE | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CellBasedAssays, ExperimentData, Preprocessing, Software, TimeCourse |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | LGPL |
| Depends | R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata, KernSmooth |
| Imports | |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | mitoODE_1.2.0.tar.gz |
| Windows Binary | mitoODE_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | mitoODE_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | mitoODE_1.2.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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