https://github.com/bioconductor-source/sepira
Science Score: 13.0%
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Low similarity (9.9%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: HTML
- Default Branch: devel
- Size: 5.04 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
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Metadata Files
README.md
SEPIRA-package
Systens EPigenomics Inference of Regulatory Activity
SEPIRA is a novel algorithm which estimates transcription factor activity in any given sample from its genome-wide mRNA expression or DNA methylation profile[1]. It encompasses two main steps:
- Construction of a tissue-specific transcription factor regulatory network, consisting of transcription factors that are more highly expressed in the user-specified tissue type (the 'tissue type of interest') compared to other tissue types, plus an associated set of high-confidence downstream targets.
- Estimation of transcription factor activity in this network, in any given dataset consisting of gene expression or promoter DNA methylation profiles.
Usage
Inferring tissue-specific network
{r eval=FALSE}
net.o <- sepiraInfNet(data=data.m, tissue=colnames(data.m), toi = "Lung", cft = "Blood",
TFs = TFeid, sdth = 0.25, sigth = 0.05, pcorth = 0.2, degth = c(0.05, 0.05),
lfcth = c(log2(1.5), 0), minNtgts = 3, ncores = 1)
** Note: data.m should be a normalized gene expression data set.
Estimating transcription factor activity
{r eval=FALSE}
sepiraRegAct(data = data.m, type = "DNAm", regnet = net.o$netTOI, norm = "z", ncores = 1)
Installation
An easy way to install SEPIRA is by facilitating the devtools R package.
```{r eval=FALSE}
install.packages("devtools")
library(devtools) installgithub("YC3/SEPIRA", buildvignettes=TRUE) ``` Alternatively, the package can also be cloned or downloaded from this github-rep, built via R CMD build and installed via the R CMD INSTALL command.
Getting started
The SEPIRA package contains a tutorial showing people how to implement SEPIRA in their work. The tutorial can be found in the package-vignette:
library(SEPIRA) vignette("SEPIRA")
Acknowledgements
Thanks to my supervisor Andrew Teschendorff for reviewing and commenting on the package and providing the code.
References
Chen Y, Widschwendter M, and Teschendorff AE. 2017. “Systems-Epigenomics Inference of Transcription Factor Activity Implicates Aryl-Hydrocarbon-Receptor Inactivation as a Key Event in Lung Cancer Development.” Genome Biol 18:236.
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
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Dependencies
- R >= 3.5.0 depends
- corpcor >= 1.6.9 imports
- limma >= 3.32.5 imports
- parallel >= 3.3.1 imports
- stats * imports
- igraph * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests