target
target: An R Package to Predict Combined Function of Transcription Factors
Science Score: 23.0%
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Repository
target: An R Package to Predict Combined Function of Transcription Factors
Basic Info
- Host: GitHub
- Owner: MahShaaban
- License: gpl-3.0
- Language: HTML
- Default Branch: master
- Homepage: https://bioconductor.org/packages/target/
- Size: 4.5 MB
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- Stars: 5
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
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Metadata Files
README.md
target
Predict Combined Function of Transcription Factors
Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013). Extend the algorithm to predict the combined function of two DNA-binding elements from comprable binding and expression data.
Installation
The target package can be installed from Bioconductor using BiocManager.
{r install_biocmanager,eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("target")
Getting started
The target package contains two simulated datasets. sim_peaks is random
peaks with random distances from the transcripts of chromosome 1 of the mm10
mouse genome. sim_transcripts is the same transcripts with random singed
statistics assigned to each. In the following two examples, we introduce
changes in these statistics to simulate conditions where two factors are
working cooperatively or competitively on the same transcripts.
```r
load libraries
library(target) ```
```r
load data
data("simpeaks") data("simtranscripts") ```
To help visualize these cases, a plotting function plot_profiles was
constructed to introduce the changes change in the statistics of the
transcripts near the n number of peaks. The source code for the function is
available in inst/extdata/plot-profiles.R which we source to use here.
The output of the function is a series of plots to visualize the statistics of
the two factors before and after introducing the changes, the peaks distances
and scores and the predicted functions of the factors individually and
combined.
```r
source the plotting function
source(system.file('extdata', 'plot-profiles.R', package = 'target')) ```
The first two inputs to the plotting function is the simulated peaks and transcripts. We chose to introduce positive changes to the statistics of the transcripts with the top 5000 nearby peaks of the two factors.
```r
simulate and plot cooperative factors
plotprofiles(simpeaks, sim_transcripts, n = 5000, change = c(3, 3)) ```
The changes introduced above are illustrated in the right upper quadrant of the scatter plot. The predicted functions of the two factors are similar, as shown by distribution function of the regulatory potential of their targets. Finally, when the targets are predicted based on the two statistics combined, the sign of the statistics product determines the direction of the factor interactions. Here, more higher ranking transcripts had positive/red/ cooperative change associated with the two factors.
References
Wang S, Sun H, Ma J, et al. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat Protoc. 2013;8(12):2502–2515. doi:10.1038/nprot.2013.150
Citation
For citing the package use:
```{r citation, warning=FALSE}
citing the package
citation("target")
Owner
- Name: Mahmoud Ahmed
- Login: MahShaaban
- Kind: user
- Location: London, UK
- Company: The Institute of Cancer Research
- Website: https://www.mahshaaban.com/
- Repositories: 6
- Profile: https://github.com/MahShaaban
Postdoc
GitHub Events
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- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| MahShaaban | m****y@s****g | 20 |
| Nitesh Turaga | n****a@g****m | 2 |
Committer Domains (Top 20 + Academic)
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Last synced: 6 months ago
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- Total issues: 0
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: 8 minutes
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
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Top Authors
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- MahShaaban (1)
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Packages
- Total packages: 1
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Total downloads:
- bioconductor 9,248 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: target
Predict Combined Function of Transcription Factors
- Homepage: https://github.com/MahShaaban/target
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/target/inst/doc/target.pdf
- License: GPL-3
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Latest release: 1.22.0
published 10 months ago