Package: mExplorer 1.0.0
mExplorer: Identifying Master Gene Regulators from Gene Expression and DNA-Binding Data
The method 'm:Explorer' associates a given list of target genes (e.g. those involved in a biological process) to gene regulators such as transcription factors. Transcription factors that bind DNA near significantly many target genes or correlate with target genes in transcriptional (microarray or RNAseq data) are selected. Selection of candidate master regulators is carried out using multinomial regression models, likelihood ratio tests and multiple testing correction. Reference: m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence. Juri Reimand, Anu Aun, Jaak Vilo, Juan M Vaquerizas, Juhan Sedman and Nicholas M Luscombe. Genome Biology (2012) 13:R55 <doi:10.1186/gb-2012-13-6-r55>.
Authors:
mExplorer_1.0.0.tar.gz
mExplorer_1.0.0.zip(r-4.5)mExplorer_1.0.0.zip(r-4.4)mExplorer_1.0.0.zip(r-4.3)
mExplorer_1.0.0.tgz(r-4.4-any)mExplorer_1.0.0.tgz(r-4.3-any)
mExplorer_1.0.0.tar.gz(r-4.5-noble)mExplorer_1.0.0.tar.gz(r-4.4-noble)
mExplorer_1.0.0.tgz(r-4.4-emscripten)mExplorer_1.0.0.tgz(r-4.3-emscripten)
mExplorer.pdf |mExplorer.html✨
mExplorer/json (API)
| # Install 'mExplorer' in R: |
| install.packages('mExplorer', repos = c('https://reimand0.r-universe.dev', 'https://cloud.r-project.org')) |
- small_test_dframe - Small sample of predictor data for testing m:Explorer
- small_test_response_vec - Small vector of yeast transcription factors for testing m:Explorer
- yeastCCgenes - Example vector of yeast transcription factors for m:Explorer
- yeastTFdata - Example predictor data for m:Explorer
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 7 years agofrom:c9c122bd2f. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | OK | Oct 31 2024 |
| R-4.5-linux | OK | Oct 31 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:mExplorerprepare_gmt_input
Dependencies:BiobaseBiocGenericsemmeansestimabilityfftwlatticelimmamvtnormnlmennetnumDerivqusagestatmod
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Selection of process-specific regulators from high-throughput data using multinomial regression models. | mExplorer |
| Creation of m:Explorer input data frame from GMT files | prepare_gmt_input |
| Small sample of predictor data for testing m:Explorer | small_test_dframe |
| Small vector of yeast transcription factors for testing m:Explorer | small_test_response_vec |
| Example vector of yeast transcription factors for m:Explorer | yeastCCgenes |
| Example predictor data for m:Explorer | yeastTFdata |
