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.

Author
Yupeng He
Date of publication
2016-06-21 09:23:58
Maintainer
Yupeng He <yupeng.he.bioinfo@gmail.com>
License
BSD_2_clause + file LICENSE
Version
1.0
URLs

View on CRAN

Man pages

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_eval_prediction
Evaluating the prediction results
REPTILE-package
Regulatory Element Prediction
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...
reptile_train
Learn a REPTILE enhancer model
reptile_train_one_mode
Internal - Learn single random forest classifier
rsd
REPTILE sample data (rsd)

Files in this package

REPTILE
REPTILE/NAMESPACE
REPTILE/data
REPTILE/data/rsd.rda
REPTILE/R
REPTILE/R/reptile_predict.R
REPTILE/R/get_option_parser_training.R
REPTILE/R/get_option_parser_compute_score.R
REPTILE/R/read_label.R
REPTILE/R/read_epigenomic_data.R
REPTILE/R/calculate_epimark_deviation.R
REPTILE/R/reptile_predict_genome_wide.R
REPTILE/R/reptile_eval_prediction.R
REPTILE/R/reptile_predict_one_mode.R
REPTILE/R/reptile_train_one_mode.R
REPTILE/R/reptile_train.R
REPTILE/R/get_option_parser_evaluation.R
REPTILE/MD5
REPTILE/DESCRIPTION
REPTILE/man
REPTILE/man/reptile_predict_one_mode.Rd
REPTILE/man/read_epigenomic_data.Rd
REPTILE/man/reptile_train.Rd
REPTILE/man/get_option_parser_training.Rd
REPTILE/man/reptile_train_one_mode.Rd
REPTILE/man/reptile_eval_prediction.Rd
REPTILE/man/REPTILE-package.Rd
REPTILE/man/rsd.Rd
REPTILE/man/get_option_parser_compute_score.Rd
REPTILE/man/reptile_predict.Rd
REPTILE/man/calculate_epimark_deviation.Rd
REPTILE/man/get_option_parser_evaluation.Rd
REPTILE/man/read_label.Rd
REPTILE/man/reptile_predict_genome_wide.Rd
REPTILE/LICENSE