tigre
Transcription factor Inference through Gaussian process Reconstruction of Expression
Bioconductor version: 2.6
The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF.
Author: Antti Honkela, Pei Gao, Jonatan Ropponen, Magnus Rattray, Neil D. Lawrence
Maintainer: Antti Honkela <antti.honkela at tkk.fi>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("tigre")
To cite this package in a publication, start R and enter:
citation("tigre")
Documentation
| R Script | tigre Quick Guide | |
| R Script | tigre User Guide | |
| tigre-009.pdf | ||
| tigre-010.pdf | ||
| Reference Manual |
Details
| biocViews | Microarray, Bioinformatics, TimeCourse, GeneExpression, Transcription |
| Depends | R (>= 2.11.0), Biobase |
| Imports | Biobase, methods, AnnotationDbi, gplots, graphics, puma, stats, utils |
| Suggests | puma, drosgenome1.db, annotate |
| System Requirements | |
| License | AGPL-3 |
| URL | http://www.bioinf.manchester.ac.uk/resources/tiger/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Version | 1.2.1 |
| Since | Bioconductor 2.6 (R-2.11) |
Package Downloads
| Package Source | tigre_1.2.1.tar.gz |
| Windows Binary | tigre_1.2.1.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | tigre_1.2.1.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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