Identification of potential riboswitch elements in Homo Sapiens mRNA 5'UTR sequences using Positive-Unlabeled machine learning
This repository contains all the final data files used for the analysis in the above manuscript.
├─ alns/ - final alignment images for the website
│ ├─ aln_%%ID%%_%%ENS_NORM%%.png
├─ data_files/ - raw/processed data files used to make the feature sets
│ ├─ CCDS_nucleotide.current_11.28.2021.fa
│ ├─ riboswitch_RNAcentral_8.19.21.json
│ ├─ rs_dot.json
│ ├─ RSid_to_ligand.json
│ ├─ 5primeUTR_final_db_2.csv
│ ├─ 5primeUTR_newutrdb_ML2.csv
│ ├─ RS_final_db.csv
│ ├─ RS_id_to_ligand.csv
│ ├─ check_new_utr.py
│ ├─ data_processor.py
│ ├─ process_rna_central_rs_json.py
│ ├─ rna_central_dot_structure_scraper.py
│ ├─ species_in_RS_set.txt
├─ elkanoto_models/ - PUlearn models
│ ├─ EKmodel_witheld_w_struct_features_9_26_%%LIGAND%%_%%LIGAND%%.joblib
│ ├─ load_ensemble.py
│ ├─ utr_proba_norm.npy
├─ ensemble_predictions/ - predictions from the ensemble classifier
│ ├─ all_utr_predictions.npy
│ ├─ final_set_436.json
│ ├─ final_set_1533.json
│ ├─ utr_dot_hits_1533.json
│ ├─ utr_proba_norm.npy
│ ├─ utr_proba_1533.npy
├─ feature_npy_files/ - extracted feature data arrays
│ ├─ X_RS_full.npy
│ ├─ X_UTR.npy
│ ├─ ids_UTR.npy
│ ├─ ids_RS.npy
├─ Figures/ ─ figure files for the paper
├─ GO/ ─ GO analysis output files
│ ├─ component_436.txt
│ ├─ component_1533.txt
│ ├─ function_436.txt
│ ├─ function_1533.txt
│ ├─ process_436.txt
│ ├─ process_1533.txt
│ ├─ gene_list_436.txt
│ ├─ gene_list_1533.txt
Read the manuscript here
Rerun the analysis here:
Contact info: wsraymon@rams.colostate.edu