REPTILE1.0 package

Regulatory DNA Element Prediction

calculate_epimark_deviation

Internal - calculating intensity deviation feature

get_option_parser_compute_score

Internal - parsing options for REPTILE_compute_score.R

get_option_parser_evaluation

Internal - parsing options for REPTILE_evaluate_prediction.R

get_option_parser_training

Internal - parsing options for REPTILE_train.R

read_epigenomic_data

Reading epigenomic data from epimark file

read_label

Reading labels of regions from label file

REPTILE-package

Regulatory Element Prediction

reptile_eval_prediction

Evaluating the prediction results

reptile_predict

Predicting enhancer activity of given regions

reptile_predict_genome_wide

Predicting enhancer activity

reptile_predict_one_mode

Internal - predicting enhancer activity of DMRs or query regions

reptile_train

Learn a REPTILE enhancer model

reptile_train_one_mode

Internal - Learn single random forest classifier

Download source packageRead PDF manual

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.