Learn R Programming

REPTILE (version 1.0)

Regulatory DNA Element Prediction

Description

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 for more information.

Copy Link

Version

Install

install.packages('REPTILE')

Monthly Downloads

253

Version

1.0

License

BSD_2_clause + file LICENSE

Issues

2

Pull Requests

0

Stars

28

Forks

4

Maintainer

Yupeng He

Last Published

June 21st, 2016

Functions in REPTILE (1.0)

read_epigenomic_data

Reading epigenomic data from epimark file
get_option_parser_compute_score

Internal - parsing options for REPTILE_compute_score.R
reptile_predict_genome_wide

Predicting enhancer activity
reptile_eval_prediction

Evaluating the prediction results
reptile_predict_one_mode

Internal - predicting enhancer activity of DMRs or query regions
calculate_epimark_deviation

Internal - calculating intensity deviation feature
reptile_predict

Predicting enhancer activity of given regions
get_option_parser_evaluation

Internal - parsing options for REPTILE_evaluate_prediction.R
get_option_parser_training

Internal - parsing options for REPTILE_train.R
read_label

Reading labels of regions from label file
REPTILE-package

Regulatory Element Prediction
reptile_train_one_mode

Internal - Learn single random forest classifier
rsd

REPTILE sample data (rsd)
reptile_train

Learn a REPTILE enhancer model