To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("tigre")
In most cases, you don't need to download the package archive at all.
tigre
Transcription factor Inference through Gaussian process Reconstruction of Expression
Bioconductor version: 3.0
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, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence
Maintainer: Antti Honkela <antti.honkela at hiit.fi>
Citation (from within R,
enter citation("tigre")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("tigre")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("tigre")
| R Script | tigre Quick Guide | |
| R Script | tigre User Guide | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bayesian, GeneExpression, GeneRegulation, Microarray, NetworkInference, Software, TimeCourse, Transcription |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) |
| License | AGPL-3 |
| Depends | R (>= 2.11.0), BiocGenerics, Biobase |
| Imports | methods, AnnotationDbi, gplots, graphics, stats, utils, annotate, DBI, RSQLite |
| LinkingTo | |
| Suggests | drosgenome1.db, puma, lumi, BiocStyle |
| SystemRequirements | |
| Enhances | |
| URL | http://www.bioinf.manchester.ac.uk/resources/tiger/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | tigre_1.20.0.tar.gz |
| Windows Binary | tigre_1.20.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | tigre_1.20.0.tgz |
| Mac OS X 10.9 (Mavericks) | tigre_1.20.0.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
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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