Package: REPTILE 1.0
REPTILE: Regulatory DNA Element Prediction
Predicting regulatory DNA elements based on epigenomic signatures. This package is more of a set of building blocks than a direct solution. REPTILE regulatory prediction pipeline is built on this R package. See <https://github.com/yupenghe/REPTILE> for more information.
Authors:
REPTILE_1.0.tar.gz
REPTILE_1.0.zip(r-4.5)REPTILE_1.0.zip(r-4.4)REPTILE_1.0.zip(r-4.3)
REPTILE_1.0.tgz(r-4.4-any)REPTILE_1.0.tgz(r-4.3-any)
REPTILE_1.0.tar.gz(r-4.5-noble)REPTILE_1.0.tar.gz(r-4.4-noble)
REPTILE_1.0.tgz(r-4.4-emscripten)REPTILE_1.0.tgz(r-4.3-emscripten)
REPTILE.pdf |REPTILE.html✨
REPTILE/json (API)
| # Install 'REPTILE' in R: |
| install.packages('REPTILE', repos = c('https://yupenghe.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yupenghe/reptile/issues
- rsd - REPTILE sample data
Last updated 8 years agofrom:88a5f5425f. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 15 2024 |
| R-4.5-win | OK | Sep 15 2024 |
| R-4.5-linux | OK | Sep 15 2024 |
| R-4.4-win | OK | Sep 15 2024 |
| R-4.4-mac | OK | Sep 15 2024 |
| R-4.3-win | OK | Sep 15 2024 |
| R-4.3-mac | OK | Sep 15 2024 |
Exports:calculate_epimark_deviationget_option_parser_compute_scoreget_option_parser_evaluationget_option_parser_trainingread_epigenomic_dataread_labelreptile_eval_predictionreptile_predictreptile_predict_genome_widereptile_predict_one_modereptile_trainreptile_train_one_mode
Dependencies:bitopscaToolscodetoolsdoParallelfluxforeachgetoptiteratorsoptparserandomForest
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Regulatory Element Prediction | REPTILE-package REPTILE |
| Internal - calculating intensity deviation feature | calculate_epimark_deviation |
| Internal - parsing options for REPTILE_compute_score.R | get_option_parser_compute_score |
| Internal - parsing options for REPTILE_evaluate_prediction.R | get_option_parser_evaluation |
| Internal - parsing options for REPTILE_train.R | get_option_parser_training |
| Reading epigenomic data from epimark file | read_epigenomic_data |
| Reading labels of regions from label file | read_label |
| Evaluating the prediction results | reptile_eval_prediction |
| Predicting enhancer activity of given regions | reptile_predict |
| Predicting enhancer activity | reptile_predict_genome_wide |
| Internal - predicting enhancer activity of DMRs or query regions | reptile_predict_one_mode |
| Learn a REPTILE enhancer model | reptile_train |
| Internal - Learn single random forest classifier | reptile_train_one_mode |
| REPTILE sample data (rsd) | rsd |
