Index C | D | E | F | G | I | L | M | P | R | S | U | V C check_modality_per_gene() (InPheC_Step2.PGMInputPreparer method) check_pkl_file_count() (InPheC_Step3.Utils static method) combine() (InPheC_Step3.PosteriorCombiner method) combine_and_add_controls() (InPheC_Step2.PGMInputPreparer method) combine_in2pgm_outposterior() (InPheC_Step3.DataProcessor method) configure_logging() (InPheC_Step3.Utils static method) CorePGM (class in InPheC_Step2) D DataLoader (class in InPheC_Step1) DataProcessor (class in InPheC_Step1) (class in InPheC_Step3) E ElasticNetProcessor (class in InPheC_Step1) estimate_a_prime() (InPheC_Step2.PGMInputPreparer method) extract() (InPheC_Step3.ParameterExtractor method) F FileNotFound filter_data() (InPheC_Step1.DataProcessor method) form_final_grn() (InPheC_Step3.DataProcessor method) G get_args() (InPheC_Step2.Step2ArgumentParser method) I InPheC_Step1 module InPheC_Step2 module InPheC_Step3 module L load_chip_data() (InPheC_Step1.DataLoader method) load_csv() (InPheC_Step2.Step1DataLoader method) load_data() (InPheC_Step2.Step1DataLoader method) load_rna_data() (InPheC_Step1.DataLoader method) load_tf_list() (InPheC_Step1.DataLoader method) logsumexp() (InPheC_Step2.CorePGM method) M module InPheC_Step1 InPheC_Step2 InPheC_Step3 P ParameterExtractor (class in InPheC_Step3) parse() (InPheC_Step3.Step3ArgumentParser static method) parse_args() (InPheC_Step1.Step1ArgumentParser method) perform_elastic_net() (InPheC_Step1.ElasticNetProcessor method) PGMInputPreparer (class in InPheC_Step2) PGMInputPreparer.beta_unif_gen (class in InPheC_Step2) PosteriorCombiner (class in InPheC_Step3) print_python_details() (InPheC_Step3.Utils static method) R run() (InPheC_Step2.CorePGM method) run_model() (InPheC_Step2.CorePGM method) S save_output_files() (in module InPheC_Step1) setup_model() (InPheC_Step2.CorePGM method) step1_main() (in module InPheC_Step1) Step1ArgumentParser (class in InPheC_Step1) Step1DataLoader (class in InPheC_Step2) step2_main() (in module InPheC_Step2) Step2ArgumentParser (class in InPheC_Step2) step3_main() (in module InPheC_Step3) Step3ArgumentParser (class in InPheC_Step3) U Utils (class in InPheC_Step3) V validate_args() (InPheC_Step2.Step2ArgumentParser method)