├── .gitignore ├── LICENSE ├── README.md ├── demo ├── RNA-Protein │ ├── RNA-Protein-Interacting.csv │ ├── SampleData-Protein-B.fasta │ └── SampleData-RNA-A.fasta ├── RNA-RNA │ ├── RNA-RNA-Interacting.csv │ ├── SampleData-lncRNA-A.fasta │ └── SampleData-miRNA-B.fasta ├── RNA-compound │ ├── RNA-small-molecule-Interacting.csv │ ├── SampleData-RNA-A.fasta │ └── Small-Moleculer.smi └── RNA-only │ ├── RNA.fasta │ └── RNA_label.csv ├── fig └── RNAincoder-Title.png ├── methods ├── Methods_all_16_methods.py └── readme.txt ├── out ├── RNA-RNA │ ├── classification_result │ │ ├── Evaluation_result.csv │ │ ├── Evaluation_result.png │ │ ├── Para_128_0.0001_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_128_0.001_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_128_0.01_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_32_0.0001_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_32_0.001_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_32_0.01_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_64_0.0001_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_64_0.001_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_64_0.01_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_96_0.0001_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_96_0.001_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ └── Para_96_0.01_100 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── encoder_rna_2.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ └── encoding_features │ │ ├── Codon related (1D)_A.csv │ │ ├── Codon related (1D)_A.npy │ │ ├── Codon related (1D)_B.csv │ │ ├── Codon related (1D)_B.npy │ │ ├── EIIP based spectrum (1D)_A.csv │ │ ├── EIIP based spectrum (1D)_A.npy │ │ ├── EIIP based spectrum (1D)_B.csv │ │ ├── EIIP based spectrum (1D)_B.npy │ │ ├── Entropy density of transcript (1D)_A.csv │ │ ├── Entropy density of transcript (1D)_A.npy │ │ ├── Entropy density of transcript (1D)_B.csv │ │ ├── Entropy density of transcript (1D)_B.npy │ │ ├── Global descriptor (1D)_A.csv │ │ ├── Global descriptor (1D)_A.npy │ │ ├── Global descriptor (1D)_B.csv │ │ ├── Global descriptor (1D)_B.npy │ │ ├── Guanine-cytosine related (1D)_A.csv │ │ ├── Guanine-cytosine related (1D)_A.npy │ │ ├── Guanine-cytosine related (1D)_B.csv │ │ ├── Guanine-cytosine related (1D)_B.npy │ │ ├── Hydrogen bond related (1D)_A.csv │ │ ├── Hydrogen bond related (1D)_A.npy │ │ ├── Hydrogen bond related (1D)_B.csv │ │ ├── Hydrogen bond related (1D)_B.npy │ │ ├── K-mer (1D)_A.csv │ │ ├── K-mer (1D)_A.npy │ │ ├── K-mer (1D)_B.csv │ │ ├── K-mer (1D)_B.npy │ │ ├── Molecular fingerprint (1D)_A.csv │ │ ├── Molecular fingerprint (1D)_A.npy │ │ ├── Molecular fingerprint (1D)_B.csv │ │ ├── Molecular fingerprint (1D)_B.npy │ │ ├── Nucleotide related (1D)_A.csv │ │ ├── Nucleotide related (1D)_A.npy │ │ ├── Nucleotide related (1D)_B.csv │ │ ├── Nucleotide related (1D)_B.npy │ │ ├── Open reading frame (1D)_A.csv │ │ ├── Open reading frame (1D)_A.npy │ │ ├── Open reading frame (1D)_B.csv │ │ ├── Open reading frame (1D)_B.npy │ │ ├── Partition coefficient (1D)_A.csv │ │ ├── Partition coefficient (1D)_A.npy │ │ ├── Partition coefficient (1D)_B.csv │ │ ├── Partition coefficient (1D)_B.npy │ │ ├── Polarizability refractivity (1D)_A.csv │ │ ├── Polarizability refractivity (1D)_A.npy │ │ ├── Polarizability refractivity (1D)_B.csv │ │ ├── Polarizability refractivity (1D)_B.npy │ │ ├── Pseudo protein related (1D)_A.csv │ │ ├── Pseudo protein related (1D)_A.npy │ │ ├── Pseudo protein related (1D)_B.csv │ │ ├── Pseudo protein related (1D)_B.npy │ │ ├── Secondary structure (1D)_A.csv │ │ ├── Secondary structure (1D)_A.npy │ │ ├── Secondary structure (1D)_B.csv │ │ ├── Secondary structure (1D)_B.npy │ │ ├── Solubility lipoaffinity (1D)_A.csv │ │ ├── Solubility lipoaffinity (1D)_A.npy │ │ ├── Solubility lipoaffinity (1D)_B.csv │ │ ├── Solubility lipoaffinity (1D)_B.npy │ │ ├── Topological indice (1D)_A.csv │ │ ├── Topological indice (1D)_A.npy │ │ ├── Topological indice (1D)_B.csv │ │ └── Topological indice (1D)_B.npy ├── RNA-compound │ ├── classification_result │ │ ├── Evaluation_result.csv │ │ ├── Evaluation_result.png │ │ ├── Para_32_0.0001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_32_0.001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_32_0.01_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_64_0.0001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_64_0.001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_64_0.01_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ └── classification_result │ │ │ ├── Evaluation_result.csv │ │ │ ├── Para_128_0.0001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ │ ├── Para_128_0.001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ │ ├── Para_128_0.01_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ │ ├── Para_32_0.0001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ │ ├── Para_32_0.001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ │ ├── Para_32_0.01_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ │ ├── Para_64_0.0001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ │ ├── Para_64_0.001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ │ ├── Para_64_0.01_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ │ ├── Para_96_0.0001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ │ ├── Para_96_0.001_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ │ └── Para_96_0.01_100 │ │ │ ├── encoder_compound.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ └── encoding_features │ │ ├── Codon related (1D)_A.csv │ │ ├── Codon related (1D)_A.npy │ │ ├── EIIP based spectrum (1D)_A.csv │ │ ├── EIIP based spectrum (1D)_A.npy │ │ ├── Entropy density of transcript (1D)_A.csv │ │ ├── Entropy density of transcript (1D)_A.npy │ │ ├── Global descriptor (1D)_A.csv │ │ ├── Global descriptor (1D)_A.npy │ │ ├── Guanine-cytosine related (1D)_A.csv │ │ ├── Guanine-cytosine related (1D)_A.npy │ │ ├── Hydrogen bond related (1D)_A.csv │ │ ├── Hydrogen bond related (1D)_A.npy │ │ ├── K-mer (1D)_A.csv │ │ ├── K-mer (1D)_A.npy │ │ ├── Molecular fingerprint (1D)_A.csv │ │ ├── Molecular fingerprint (1D)_A.npy │ │ ├── MoleculerResult.csv │ │ ├── Nucleotide related (1D)_A.csv │ │ ├── Nucleotide related (1D)_A.npy │ │ ├── Open reading frame (1D)_A.csv │ │ ├── Open reading frame (1D)_A.npy │ │ ├── Partition coefficient (1D)_A.csv │ │ ├── Partition coefficient (1D)_A.npy │ │ ├── Polarizability refractivity (1D)_A.csv │ │ ├── Polarizability refractivity (1D)_A.npy │ │ ├── Pseudo protein related (1D)_A.csv │ │ ├── Pseudo protein related (1D)_A.npy │ │ ├── Secondary structure (1D)_A.csv │ │ ├── Secondary structure (1D)_A.npy │ │ ├── Solubility lipoaffinity (1D)_A.csv │ │ ├── Solubility lipoaffinity (1D)_A.npy │ │ ├── Topological indice (1D)_A.csv │ │ ├── Topological indice (1D)_A.npy │ │ ├── compound_B.csv │ │ └── compound_B.npy ├── RNA-pro │ ├── classification_result │ │ ├── Para_32_0.0001_100 │ │ │ ├── encoder_pro.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_32_0.001_100 │ │ │ ├── encoder_pro.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_32_0.01_100 │ │ │ ├── encoder_pro.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_64_0.0001_100 │ │ │ ├── encoder_pro.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ ├── Para_64_0.001_100 │ │ │ ├── encoder_pro.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ │ └── Para_64_0.01_100 │ │ │ ├── encoder_pro.h5 │ │ │ ├── encoder_rna_1.h5 │ │ │ ├── test_feature_B_encode.npy │ │ │ ├── test_feature_RNA_encode.npy │ │ │ ├── train_feature_B_encode.npy │ │ │ └── train_feature_RNA_encode.npy │ └── encoding_features │ │ ├── Codon related (1D)_A.csv │ │ ├── Codon related (1D)_A.npy │ │ ├── EIIP based spectrum (1D)_A.csv │ │ ├── EIIP based spectrum (1D)_A.npy │ │ ├── Entropy density of transcript (1D)_A.csv │ │ ├── Entropy density of transcript (1D)_A.npy │ │ ├── Global descriptor (1D)_A.csv │ │ ├── Global descriptor (1D)_A.npy │ │ ├── Guanine-cytosine related (1D)_A.csv │ │ ├── Guanine-cytosine related (1D)_A.npy │ │ ├── Hydrogen bond related (1D)_A.csv │ │ ├── Hydrogen bond related (1D)_A.npy │ │ ├── K-mer (1D)_A.csv │ │ ├── K-mer (1D)_A.npy │ │ ├── Molecular fingerprint (1D)_A.csv │ │ ├── Molecular fingerprint (1D)_A.npy │ │ ├── Nucleotide related (1D)_A.csv │ │ ├── Nucleotide related (1D)_A.npy │ │ ├── Open reading frame (1D)_A.csv │ │ ├── Open reading frame (1D)_A.npy │ │ ├── Partition coefficient (1D)_A.csv │ │ ├── Partition coefficient (1D)_A.npy │ │ ├── Polarizability refractivity (1D)_A.csv │ │ ├── Polarizability refractivity (1D)_A.npy │ │ ├── Pseudo protein related (1D)_A.csv │ │ ├── Pseudo protein related (1D)_A.npy │ │ ├── Secondary structure (1D)_A.csv │ │ ├── Secondary structure (1D)_A.npy │ │ ├── Solubility lipoaffinity (1D)_A.csv │ │ ├── Solubility lipoaffinity (1D)_A.npy │ │ ├── Topological indice (1D)_A.csv │ │ ├── Topological indice (1D)_A.npy │ │ ├── protein_B.csv │ │ └── protein_B.npy └── RNAonly │ ├── classification_result │ ├── Evaluation_result.csv │ ├── Evaluation_result.png │ ├── Para_128_0.0001_100 │ │ └── encoder_rna_1.h5 │ ├── Para_128_0.001_100 │ │ └── encoder_rna_1.h5 │ ├── Para_128_0.01_100 │ │ └── encoder_rna_1.h5 │ ├── Para_32_0.0001_100 │ │ └── encoder_rna_1.h5 │ ├── Para_32_0.001_100 │ │ └── encoder_rna_1.h5 │ ├── Para_32_0.01_100 │ │ └── encoder_rna_1.h5 │ ├── Para_64_0.0001_100 │ │ └── encoder_rna_1.h5 │ ├── Para_64_0.001_100 │ │ └── encoder_rna_1.h5 │ ├── Para_64_0.01_100 │ │ └── encoder_rna_1.h5 │ ├── Para_96_0.0001_100 │ │ └── encoder_rna_1.h5 │ ├── Para_96_0.001_100 │ │ └── encoder_rna_1.h5 │ └── Para_96_0.01_100 │ │ └── encoder_rna_1.h5 │ └── encoding_features │ ├── Codon related (1D).csv │ ├── Codon related (1D).npy │ ├── EIIP based spectrum (1D).csv │ ├── EIIP based spectrum (1D).npy │ ├── Entropy density of transcript (1D).csv │ ├── Entropy density of transcript (1D).npy │ ├── Global descriptor (1D).csv │ ├── Global descriptor (1D).npy │ ├── Guanine-cytosine related (1D).csv │ ├── Guanine-cytosine related (1D).npy │ ├── Hydrogen bond related (1D).csv │ ├── Hydrogen bond related (1D).npy │ ├── K-mer (1D).csv │ ├── K-mer (1D).npy │ ├── Molecular fingerprint (1D).csv │ ├── Molecular fingerprint (1D).npy │ ├── Nucleotide related (1D).csv │ ├── Nucleotide related (1D).npy │ ├── Open reading frame (1D).csv │ ├── Open reading frame (1D).npy │ ├── Partition coefficient (1D).csv │ ├── Partition coefficient (1D).npy │ ├── Polarizability refractivity (1D).csv │ ├── Polarizability refractivity (1D).npy │ ├── Pseudo protein related (1D).csv │ ├── Pseudo protein related (1D).npy │ ├── Secondary structure (1D).csv │ ├── Secondary structure (1D).npy │ ├── Sequence-intrinsic Features_One-hot encoding (2D).npy │ ├── Solubility lipoaffinity (1D).csv │ ├── Solubility lipoaffinity (1D).npy │ ├── Sparse encoding (2D).npy │ ├── Structure-based Features_One-hot encoding (2D).npy │ ├── Topological indice (1D).csv │ └── Topological indice (1D).npy ├── requirements.txt ├── rnaincoder.py └── utility ├── RNAcoding_01.py └── model.py /.gitignore: -------------------------------------------------------------------------------- 1 | */__pycache__ -------------------------------------------------------------------------------- /demo/RNA-Protein/RNA-Protein-Interacting.csv: -------------------------------------------------------------------------------- 1 | A,B,Label 2 | >1FFK_9,>1FFK_D,1 3 | >1FFK_0,>1FFK_I,1 4 | >1FFK_9,>1FFK_T,1 5 | >1FFK_0,>1FFK_Z,1 6 | >1GIY_A,>1GIY_C,1 7 | >1GIY_A,>1GIY_D,1 8 | >1GIY_A,>1GIY_K,1 9 | >1GIY_A,>1GIY_L,1 10 | >1GIY_A,>1GIY_N,1 11 | >1GIY_A,>1GIY_S,1 12 | >1P85_0,>1P85_H,1 13 | >1P85_0,>1P85_I,1 14 | >1P85_0,>1P85_K,1 15 | >1P85_0,>1P85_N,1 16 | >1P85_0,>1P85_R,1 17 | >1P85_0,>1P85_S,1 18 | >1P85_0,>1P85_W,1 19 | >1P85_0,>1P85_X,1 20 | >1P85_0,>1P85_1,1 21 | >2FTC_R,>2FTC_A,1 22 | >1GIY_B,>1GIY_X,0 23 | >1P85_9,>1P85_A,0 24 | >1P85_9,>1P85_B,0 25 | >1P85_9,>1P85_C,0 26 | >1P85_9,>1P85_D,0 27 | >1P85_9,>1P85_E,0 28 | >1P85_9,>1P85_G,0 29 | >1P85_9,>1P85_H,0 30 | >1P85_9,>1P85_I,0 31 | >1P85_9,>1P85_J,0 32 | >1P85_9,>1P85_K,0 33 | >1P85_9,>1P85_L,0 34 | >1P85_9,>1P85_M,0 35 | >1P85_9,>1P85_N,0 36 | >1P85_9,>1P85_O,0 37 | >1P85_9,>1P85_Q,0 38 | >1P85_9,>1P85_R,0 39 | >1P85_9,>1P85_S,0 40 | >1P85_9,>1P85_W,0 41 | >1P85_9,>1P85_X,0 42 | -------------------------------------------------------------------------------- /demo/RNA-Protein/SampleData-Protein-B.fasta: -------------------------------------------------------------------------------- 1 | >1FFK_D 2 | SSESESGGDFHEMREPRIEKVVVHMGIGHGGRDLANAEDILGEITGQMPVRTKAKRTVGEFDIREGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGVEEHTEFPSQEYDPSIGIYGLDVTVNLVRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEVSE 3 | >1FFK_I 4 | MKSMYAYIREAWKRPYEGYVGELMWHRLQKWRREPAVVRIPRPTRLDRARALGYKAKKGIIVVRVRIRRGGRRATRPNKGRKSKKMMVNRRPRKKNLQWIAEERANRKYPNMEVLNSYWVGEDGRYKWFEVILVDRDHPAIKSDPQLSWVSRTRGRVYRGLTSAGRKARGLRRKGRGAEKVRPSLRANFRKKRR 5 | >1FFK_T 6 | MHALVQLRGEVNMHTDIQDTLEMLNIHHVNHCTLVPETDAYRGMVAKVNDFVAFGEPSQETLETVLATRAEPLEGDADVDDEWVAEHTDYDDISGLAFALLSEETTLREQGLSPTLRLHPPRGGHDGVKHPVKEGGQLGKHDTEGIDDLLEAMR 7 | >1FFK_Z 8 | MQMPRRFNTYCPHCNEHQEHEVEKVRSGRQTGMKWIDRQRERNSGIGNDGKFSKVPGGDKPTKKTDLKYRCGECGKAHLREGWRAGRLEFQE 9 | >1GIY_C 10 | PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 11 | >1GIY_D 12 | QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGMEIMSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGEVRMILGKCRATVGEVGNGGRTDKPFVKAGNKHHKMKARGTKWPNVRGVAMNAVDHPFG 13 | >1GIY_K 14 | MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQKEQRQAAEELANAKKLKEQLEKLTVTIPAKAGEGGRLFGSITSKQIAESLQAQHGLKLDKRKIELADAIRALGYTNVPVKLHPEVTATLKVHVTEQK 15 | >1GIY_L 16 | MAKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVVD 17 | >1GIY_N 18 | MIQQESRLKVADNSGAREVLVIKVLGGSGRRYANIGDVVVATVKDATPGGVVKKGQVVKAVVVRTKRGVRRPDGSYIRFDENACVIIRDDKSPRGTRIFGPVARELRDKDFMKIISLAPEVI 19 | >1GIY_S 20 | MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKVLESAAANAVNNHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRTSHITVILGEKHGK 21 | >1P85_H 22 | MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI 23 | >1P85_I 24 | MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKAVVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAPEVL 25 | >1P85_K 26 | MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM 27 | >1P85_N 28 | SNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVFQTHSPVVDSISVKRRGAVRKAKLYYLRERTGKAARIKERLN 29 | >1P85_R 30 | MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNLDFVGGAE 31 | >1P85_S 32 | AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETIK 33 | >1P85_W 34 | MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA 35 | >1P85_X 36 | AKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE 37 | >1P85_1 38 | AKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK 39 | >2FTC_A 40 | LDLTLDMALGKKKNVEPFTSVLSLPYPFASEINKVAVFTENASEVKIAEENGAAFAGGTSLIQKIWDDEIVADFYVAVPEIMPELNRLRKKLNKKYPKLSRNSIGRDIPKMLELFKNGHEIKVDEERENFLQTKIATLDMSSDQIAANLQAVINEVCRHRPLNLGPFVVRAFLRSSTSEGLLLKIDPLL 41 | >1GIY_X 42 | MPRLKVKLVKSPIGYPKDQKAALKALGLRRLQQERVLEDTPAIRGNVEKVAHLVRVEVVE 43 | >1P85_A 44 | AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK 45 | >1P85_B 46 | MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA 47 | >1P85_C 48 | MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA 49 | >1P85_D 50 | AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK 51 | >1P85_E 52 | SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK 53 | >1P85_G 54 | AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVED 55 | >1P85_J 56 | MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE 57 | >1P85_L 58 | MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSEKAEAAAE 59 | >1P85_M 60 | MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF 61 | >1P85_O 62 | ARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWIARINAAARQNGISYSKFINGLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA 63 | >1P85_Q 64 | METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRTSHITVVVSDR 65 | -------------------------------------------------------------------------------- /demo/RNA-RNA/RNA-RNA-Interacting.csv: -------------------------------------------------------------------------------- 1 | A,B,Label 2 | >ENST00000453875.5,>hsa.miR.222.3p,1 3 | >ENST00000504748.1,>hsa.miR.34c.5p,1 4 | >ENST00000599755.5,>hsa.miR.497.5p,1 5 | >ENST00000454129.5,>hsa.miR.17.5p,1 6 | >ENST00000436656.5,>hsa.miR.223.3p,1 7 | >ENST00000511893.1,>hsa.miR.29b.3p,1 8 | >ENST00000414894.1,>hsa.miR.301a.3p,1 9 | >ENST00000602587.5,>hsa.miR.29b.3p,1 10 | >ENST00000584485.1,>hsa.miR.139.5p,1 11 | >ENST00000444126.5,>hsa.miR.106a.5p,1 12 | >ENST00000628924.1,>hsa.miR.20b.5p,1 13 | >ENST00000563777.1,>hsa.miR.876.5p,1 14 | >ENST00000508266.1,>hsa.miR.544a,1 15 | >ENST00000517774.1,>hsa.miR.24.3p,1 16 | >ENST00000454129.5,>hsa.miR.3619.5p,1 17 | >ENST00000602498.1,>hsa.miR.148b.3p,1 18 | >ENST00000476405.1,>hsa.miR.199b.5p,1 19 | >ENST00000411861.5,>hsa.miR.29b.3p,1 20 | >ENST00000560706.5,>hsa.miR.26b.5p,1 21 | >ENST00000449589.5,>hsa.miR.544a,1 22 | >ENST00000451786.5,>hsa.miR.450a.5p,0 23 | >ENST00000499180.2,>hsa.miR.429,0 24 | >ENST00000515108.1,>hsa.miR.122.5p,0 25 | >ENST00000508913.5,>hsa.miR.302a.3p,0 26 | >ENST00000426529.6,>hsa.miR.448,0 27 | >ENST00000382215.3,>hsa.miR.490.3p,0 28 | >ENST00000501008.2,>hsa.miR.302d.3p,0 29 | >ENST00000438608.5,>hsa.miR.149.5p,0 30 | >ENST00000398461.5,>hsa.miR.491.5p,0 31 | >ENST00000590274.1,>hsa.miR.155.5p,0 32 | >ENST00000413421.5,>hsa.miR.122.5p,0 33 | >ENST00000517675.1,>hsa.miR.302a.3p,0 34 | >ENST00000602618.1,>hsa.miR.302a.3p,0 35 | >ENST00000577163.1,>hsa.miR.302d.3p,0 36 | >ENST00000487102.5,>hsa.miR.505.3p,0 37 | >ENST00000541775.5,>hsa.miR.302d.3p,0 38 | >ENST00000409898.2,>hsa.miR.149.5p,0 39 | >ENST00000577661.1,>hsa.miR.496,0 40 | >ENST00000547799.5,>hsa.miR.192.5p,0 41 | >ENST00000458228.5,>hsa.miR.491.5p,0 42 | -------------------------------------------------------------------------------- /demo/RNA-RNA/SampleData-miRNA-B.fasta: -------------------------------------------------------------------------------- 1 | >hsa.miR.222.3p 2 | AGCTACATCTGGCTACTGGGT 3 | >hsa.miR.34c.5p 4 | AGGCAGTGTAGTTAGCTGATTGC 5 | >hsa.miR.497.5p 6 | CAGCAGCACACTGTGGTTTGT 7 | >hsa.miR.17.5p 8 | CAAAGTGCTTACAGTGCAGGTAG 9 | >hsa.miR.223.3p 10 | TGTCAGTTTGTCAAATACCCCA 11 | >hsa.miR.29b.3p 12 | TAGCACCATTTGAAATCAGTGTT 13 | >hsa.miR.301a.3p 14 | CAGTGCAATAGTATTGTCAAAGC 15 | >hsa.miR.139.5p 16 | TCTACAGTGCACGTGTCTCCAGT 17 | >hsa.miR.106a.5p 18 | AAAAGTGCTTACAGTGCAGGTAG 19 | >hsa.miR.20b.5p 20 | CAAAGTGCTCATAGTGCAGGTAG 21 | >hsa.miR.876.5p 22 | TGGATTTCTTTGTGAATCACCA 23 | >hsa.miR.544a 24 | ATTCTGCATTTTTAGCAAGTTC 25 | >hsa.miR.24.3p 26 | TGGCTCAGTTCAGCAGGAACAG 27 | >hsa.miR.3619.5p 28 | TCAGCAGGCAGGCTGGTGCAGC 29 | >hsa.miR.148b.3p 30 | TCAGTGCATCACAGAACTTTGT 31 | >hsa.miR.199b.5p 32 | CCCAGTGTTTAGACTATCTGTTC 33 | >hsa.miR.26b.5p 34 | TTCAAGTAATTCAGGATAGGT 35 | >hsa.miR.450a.5p 36 | TTTTGCGATGTGTTCCTAATAT 37 | >hsa.miR.429 38 | TAATACTGTCTGGTAAAACCGT 39 | >hsa.miR.122.5p 40 | TGGAGTGTGACAATGGTGTTTG 41 | >hsa.miR.302a.3p 42 | TAAGTGCTTCCATGTTTTGGTGA 43 | >hsa.miR.448 44 | TTGCATATGTAGGATGTCCCAT 45 | >hsa.miR.490.3p 46 | CAACCTGGAGGACTCCATGCTG 47 | >hsa.miR.302d.3p 48 | TAAGTGCTTCCATGTTTGAGTGT 49 | >hsa.miR.149.5p 50 | TCTGGCTCCGTGTCTTCACTCCC 51 | >hsa.miR.491.5p 52 | AGTGGGGAACCCTTCCATGAGG 53 | >hsa.miR.155.5p 54 | TTAATGCTAATCGTGATAGGGGTT 55 | >hsa.miR.505.3p 56 | CGTCAACACTTGCTGGTTTCCT 57 | >hsa.miR.496 58 | TGAGTATTACATGGCCAATCTC 59 | >hsa.miR.192.5p 60 | CTGACCTATGAATTGACAGCC 61 | -------------------------------------------------------------------------------- /demo/RNA-compound/RNA-small-molecule-Interacting.csv: -------------------------------------------------------------------------------- 1 | A,B,Label 2 | >2FCX,XXX,1 3 | >1BYJ,GE1,1 4 | >1XPF,SPM,1 5 | >1AJU,ARG,1 6 | >2ET3,LLL,1 7 | >1LVJ,PMZ,1 8 | >1NBK,GND,1 9 | >2B57,6AP,1 10 | >1EI2,NMY,1 11 | >1RAW,AMP,1 12 | >1TOB,TOA,1 13 | >1FYP,PAR,1 14 | >1QD3,BDG,1 15 | >2CKY,TPP,1 16 | >2OE8,AM2,1 17 | >2GDI,TPP,1 18 | >2BEE,JS4,1 19 | >1ZZ5,CNY,1 20 | >2F4U,AB6,1 21 | >1KOD,CIR,1 22 | >2BE0,JS5,1 23 | >2AU4,GTP,1 24 | >1Q8N,MGR,1 25 | >2OE5,AM2,1 26 | >1EI2,NMY,1 27 | >1NTA,SRY,1 28 | >2FCZ,RIO,1 29 | >1FUF,SPM,1 30 | >2BEE,JS4,1 31 | >1KOD,CIR,1 32 | >1YRJ,AM2,1 33 | >1PBR,PA1,1 34 | >1KOC,ARG,1 35 | >2PWT,LHA,1 36 | >2ET8,XXX,1 37 | >1LC4,TOY,1 38 | >1AJU,ARG,1 39 | >1O9M,42B,1 40 | >2F4S,XXX,1 41 | >1FMN,FMN,1 42 | >2FD0,LIV,1 43 | >3D2X,D2X,1 44 | >2ET4,NMY,1 45 | >1NBK,GND,1 46 | >1KOC,ARG,1 47 | >1XPF,SPM,0 48 | >1EHT,TEP,0 49 | >1Q8N,MGR,0 50 | >1F1T,ROS,0 51 | >1J7T,PAR,0 52 | >2BE0,JS5,0 53 | >1NTB,SRY,0 54 | >1J7T,PAR,0 55 | >1YKV,DAI,0 56 | >1MWL,GET,0 57 | >2TOB,TOY,0 58 | >2OGN,G80,0 59 | >1XBP,MUL,0 60 | >1F27,BTN,0 61 | >2FD0,LIV,0 62 | >1NEM,BDG,0 63 | >1AM0,AMP,0 64 | >2G9C,3AY,0 65 | >2TOB,TOA,0 66 | >1AM0,AMP,0 67 | >2ESJ,LIV,0 68 | >2F4U,AB6,0 69 | >1F27,BTN,0 70 | >2GIS,SAM,0 71 | >2ET8,XXX,0 72 | >1TOB,TOY,0 73 | >1Y27,GUN,0 74 | >1O15,TEP,0 75 | >2FCZ,RIO,0 76 | >1FYP,PAR,0 77 | >1NEM,PAR,0 78 | >1HNW,TAC,0 79 | >1Y26,ADE,0 80 | >2O3X,N30,0 81 | >1PBR,PAR,0 82 | >3GX2,SFG,0 83 | >1MWL,GET,0 84 | >1Y26,ADE,0 85 | >3SUX,THF,0 86 | >4FE5,HPA,0 87 | >1F1T,ROS,0 88 | >2OE5,AM2,0 89 | >1BYJ,LLL,0 90 | >1FJG,SCM,0 91 | >1EHT,TEP,0 92 | -------------------------------------------------------------------------------- /demo/RNA-compound/Small-Moleculer.smi: -------------------------------------------------------------------------------- 1 | Cn1c(=O)c2[nH]cnc2n(C)c1=O TEP 2 | NCCCNCCCCNCCCN SPM 3 | NCCC(O)C(=O)NC1CC(N)C(OC2OC(CO)C(O)C(O)C2N)C(OC2OC(CO)C(OC3OC(CN)C(O)C(O)C3N)C2OCCNCCc2ccccc2)C1O LHA 4 | CN(C)C1C(O)=C(C(N)=O)C(=O)C2(O)C(O)=C3C(=O)c4c(O)cccc4C(C)(O)C3CC12 TAC 5 | CC(=O)c1ccc2c(c1)N(CCCN(C)C)c1ccccc1S2 PMZ 6 | NCC1OC(OC2C(N)CC(N)C(OC3OC(CO)C(O)C(N)C3O)C2O)C(N)CC1O TOY 7 | Cc1ncc(C[n+]2csc(CCOP(=O)(O)OP(=O)(O)O)c2C)c(O)n1 D2X 8 | CNC1C(O)C(OC2C(N)CC(N)C(OC3OC(CN)CCC3N)C2O)OCC1(C)O LLL 9 | Nc1nc2c(ncn2C2OC(COP(=O)(O)OP(=O)(O)OP(=O)(O)O)C(O)C2O)c(=O)[nH]1 GTP 10 | CNC1C(OC2OC(CO)C(N)C(O)C2O)OC2CC(N)C(OC3C(N)CC(N)C(O)C3O)OC2C1O AM2 11 | CCCCCN1C(=O)C2C3c4ccccc4C(CO)(c4ccccc43)C2C1=O DAI 12 | NCC1OC(OC2C(O)C(N)CC(N)C2OC2OC(CO)C(O)C(O)C2N)C(O)C1O N30 13 | Nc1nc2[nH]cnc2c(=O)[nH]1 GUN 14 | NCCCNCCOC1C(NC(=O)C(O)CCN)CC(N)C(OC2OC(CO)C(O)C(O)C2N)C1O AB6 15 | Nc1nc(=O)c2c([nH]1)N=CC(CNc1ccc(C(=O)NC(CCC(=O)O)C(=O)O)cc1)N2CO THF 16 | NCC1OC(OC2C(CO)OC(OC3C(O)C(N)CC(N)C3OC3OC(CO)C(O)C(O)C3N)C2O)C(N)C(O)C1O PAR 17 | NC(=[NH2+])NCCCC(N)C(=O)O ARG 18 | NCC1OC(O)C(N)C(O)C1O BDG 19 | O=C(O)CCCCC1SCC2NC(=O)NC21 BTN 20 | NCC1CCC(N)C(O)O1 GE1 21 | CNC1C(O)C(NC)C2OC3(O)C(=O)CC(C)OC3OC2C1O SCM 22 | Nc1ncnc2c1ncn2C1OC(CC(N)CCC(N)C(=O)O)C(O)C1O SFG 23 | NC(=O)NCCCC(N)C(=O)O CIR 24 | O=c1[nH]cnc2nc[nH]c12 HPA 25 | NCC1OC(OC2C(CO)OC(OC3C(O)C(N)CC(N)C3OC3OC(CO)C(O)C(O)C3N)C2OCCNCC2CCCNC2)C(N)C(O)C1O JS5 26 | NCCC(O)C(=O)O 42B 27 | N=C(N)NCCCC([NH3+])C(=O)O GND 28 | CNC1C(O)C(OC2C(N)CC(N)C(OC3OC(C(C)O)C(O)C(O)C3N)C2O)OCC1(C)O GET 29 | Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(CC(O)C(O)C(O)COP(=O)(O)O)c2cc1C FMN 30 | NCC1OC(OC2C3CNC4C(OC(CN)C(O)C4O)OC4C(N)CC(N)C(O)C4OC(O3)C2O)C(N)C(O)C1O CNY 31 | Nc1ncnc2[nH]cnc12 ADE 32 | NCC1OC(OC2C(N)CC(N)C(O)C2OC2OC(CO)C(O)C2O)C(N)C(O)C1O RIO 33 | Nc1nc(N)c2nc[nH]c2n1 6AP 34 | Nc1cc(N)nc(N)n1 3AY 35 | CN(C)c1ccc2c(-c3ccccc3)c3ccc(=[N+](C)C)cc-3oc2c1 ROS 36 | NCCCNCCOC1C(OC2C(O)C(N)CC(N)C2OC2OC(CO)C(O)C(O)C2N)OC(CO)C1OC1OC(CN)C(O)C(O)C1N JS4 37 | NCC1OC(OC2C(CO)OC(OC3C(O)C(N)CC(N)C3OC3OC(CO)C(O)CC3N)C2O)C(N)C(O)C1OC1OC(CO)C(O)C(O)C1O LIV 38 | C=CC1(C)CC(OC(=O)CSCCN(CC)CC)C2(C)C(C)CCC3(CCC(=O)C32)C(C)C1O MUL 39 | NCC1OC(OC2C(CO)OC(OC3C(O)C(N)CC(N)C3OC3OC(CN)C(O)C(O)C3N)C2O)C(N)C(O)C1O NMY 40 | NCC1OC(OC2C(N)CC(N)C(O)C2O)C(N)C(O)C1O XXX 41 | NC1C(O)OC(CO)C(O)C1O PA1 42 | C=CC1(C)CC(OC(=O)CSC2CCNCC2)C2(C)C(C)CCC3(CCC(=O)C32)C(C)C1O G80 43 | Cc1ncc(C[n+]2csc(CCOP(=O)(O)OP(=O)(O)O)c2C)c(N)n1 TPP 44 | CNC1C(OC2C(OC3C(O)C(O)C(NC(=N)N)C(O)C3NC(=N)N)OC(C)C2(O)C=O)OC(CO)C(O)C1O SRY 45 | [NH3+]C1C(O)C(O)OC(CO)C1O TOA 46 | C[S+](CCC(N)C(=O)[O-])CC1OC(n2cnc3c(N)ncnc32)C(O)C1O SAM 47 | CN(C)c1ccc(C(=C2C=CC(=[N+](C)C)C=C2)c2ccccc2)cc1 MGR 48 | Nc1ncnc2c1ncn2C1OC(COP(=O)(O)O)C(O)C1O AMP 49 | -------------------------------------------------------------------------------- /demo/RNA-only/RNA_label.csv: -------------------------------------------------------------------------------- 1 | Seqname,Label 2 | >ENST00000329743.3,0 3 | >ENST00000332881.3,0 4 | >ENST00000333139.3,0 5 | >ENST00000354376.3,0 6 | >ENST00000360656.2,0 7 | >ENST00000364140.1,0 8 | >ENST00000366188.2,0 9 | >ENST00000366424.2,0 10 | >ENST00000367276.8,0 11 | >ENST00000367563.7,0 12 | >gi|1000814511|ref|NM_001320453.1|,1 13 | >gi|1001184398|ref|NM_001320455.1|,1 14 | >gi|1002623418|ref|NM_001320679.1|,1 15 | >gi|1006456381|ref|NM_001321205.1|,1 16 | >gi|1007378466|ref|NM_001321202.1|,1 17 | >gi|1010221562|ref|NM_001321553.1|,1 18 | >gi|1010223708|ref|NM_001321552.1|,1 19 | >gi|1012282594|ref|NM_001321706.1|,1 20 | >gi|1013071015|ref|NM_001025591.3|,1 21 | >gi|1013071031|ref|NM_001321918.1|,1 22 | -------------------------------------------------------------------------------- /fig/RNAincoder-Title.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idrblab/rnaincoder/9a9db569eb359db493eddf9ba86d5e7a3b9050ef/fig/RNAincoder-Title.png -------------------------------------------------------------------------------- /methods/readme.txt: -------------------------------------------------------------------------------- 1 | Because the file in this folder is too large, please download the compressed file from http://idrblab.org/rnaincoder/download/methods.zip and decompress it in this folder. -------------------------------------------------------------------------------- /out/RNA-RNA/classification_result/Evaluation_result.csv: -------------------------------------------------------------------------------- 1 | ,embedding parameters,best parameters,Acc,Sn,Sp,Pre,MCC,AUC 2 | 1,"[32, 0.0001, 100]",{'n_estimators': 170},1.0,1.0,1.0,1.0,1.0,1.0 3 | 2,"[32, 0.001, 100]",{'n_estimators': 70},1.0,1.0,1.0,1.0,1.0,1.0 4 | 3,"[32, 0.01, 100]",{'n_estimators': 70},1.0,1.0,1.0,1.0,1.0,1.0 5 | 4,"[64, 0.0001, 100]",{'n_estimators': 170},1.0,1.0,1.0,1.0,1.0,1.0 6 | 5,"[64, 0.001, 100]",{'n_estimators': 70},1.0,1.0,1.0,1.0,1.0,1.0 7 | 6,"[64, 0.01, 100]",{'n_estimators': 170},1.0,1.0,1.0,1.0,1.0,1.0 8 | 7,"[96, 0.0001, 100]",{'n_estimators': 170},1.0,1.0,1.0,1.0,1.0,1.0 9 | 8,"[96, 0.001, 100]",{'n_estimators': 70},1.0,1.0,1.0,1.0,1.0,1.0 10 | 9,"[96, 0.01, 100]",{'n_estimators': 170},1.0,1.0,1.0,1.0,1.0,1.0 11 | 10,"[128, 0.0001, 100]",{'n_estimators': 70},1.0,1.0,1.0,1.0,1.0,1.0 12 | 11,"[128, 0.001, 100]",{'n_estimators': 170},1.0,1.0,1.0,1.0,1.0,1.0 13 | 12,"[128, 0.01, 100]",{'n_estimators': 170},1.0,1.0,1.0,1.0,1.0,1.0 14 | -------------------------------------------------------------------------------- /out/RNA-RNA/classification_result/Evaluation_result.png: -------------------------------------------------------------------------------- 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28,hsa.miR.491.5p,0.009476,0.29242,0.032406,0.066275,0.066275,0.066275,0.066275,0.066275 31 | 29,hsa.miR.155.5p,0.016333,0.337043,0.048459,0.04019,0.04019,0.04019,0.04019,0.04019 32 | 30,hsa.miR.122.5p,0.032817,0.282505,0.116164,0.05641,0.05641,0.05641,0.05641,0.05641 33 | 31,hsa.miR.302a.3p,0.036335,0.334573,0.108601,0.036335,0.036335,0.036335,0.036335,0.036335 34 | 32,hsa.miR.302a.3p,0.036335,0.334573,0.108601,0.036335,0.036335,0.036335,0.036335,0.036335 35 | 33,hsa.miR.302d.3p,0.012068,0.334573,0.036071,0.037822,0.037822,0.037822,0.037822,0.037822 36 | 34,hsa.miR.505.3p,0.020112,0.341883,0.058828,0.020112,0.020112,0.020112,0.020112,0.020112 37 | 35,hsa.miR.302d.3p,0.012068,0.334573,0.036071,0.037822,0.037822,0.037822,0.037822,0.037822 38 | 36,hsa.miR.149.5p,0.013782,0.363999,0.037861,0.024229,0.024229,0.024229,0.024229,0.024229 39 | 37,hsa.miR.496,0.015213,0.335777,0.045307,0.032287,0.032287,0.032287,0.032287,0.032287 40 | 38,hsa.miR.192.5p,0.023097,0.318089,0.072613,0.023537,0.023537,0.023537,0.023537,0.023537 41 | 39,hsa.miR.491.5p,0.009476,0.29242,0.032406,0.066275,0.066275,0.066275,0.066275,0.066275 42 | -------------------------------------------------------------------------------- /out/RNA-RNA/encoding_features/EIIP based spectrum (1D)_B.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idrblab/rnaincoder/9a9db569eb359db493eddf9ba86d5e7a3b9050ef/out/RNA-RNA/encoding_features/EIIP based spectrum (1D)_B.npy -------------------------------------------------------------------------------- /out/RNA-RNA/encoding_features/Entropy density of transcript (1D)_A.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idrblab/rnaincoder/9a9db569eb359db493eddf9ba86d5e7a3b9050ef/out/RNA-RNA/encoding_features/Entropy density of transcript (1D)_A.npy -------------------------------------------------------------------------------- /out/RNA-RNA/encoding_features/Entropy density of transcript (1D)_B.csv: -------------------------------------------------------------------------------- 1 | ,B,TraEA: Entropy density A on transcript,TraEC: Entropy density C on transcript,TraED: Entropy density D on transcript,TraEE: Entropy density E on transcript,TraEF: Entropy density F on transcript,TraEG: Entropy density G on transcript,TraEH: Entropy density H on transcript,TraEI: Entropy density I on transcript,TraEK: Entropy density K on transcript,TraEL: Entropy density L on transcript,TraEM: Entropy density M on transcript,TraEN: Entropy density N on transcript,TraEP: Entropy density P on transcript,TraEQ: Entropy density Q on transcript,TraER: Entropy density R on transcript,TraES: Entropy density S on transcript,TraET: Entropy density T on transcript,TraEV: Entropy density V on transcript,TraEW: Entropy density W on transcript,TraEY: Entropy density Y on transcript 2 | 0,hsa.miR.222.3p,0.0,0.0,0.0,0.0,0.0,0.159044,0.0,0.159044,0.0,0.204782,0.0,0.0,0.0,0.0,0.0,0.159044,0.0,0.0,0.159044,0.159044 3 | 1,hsa.miR.34c.5p,0.0,0.166667,0.0,0.0,0.0,0.0,0.0,0.166667,0.0,0.166667,0.0,0.0,0.0,0.166667,0.166667,0.166667,0.0,0.0,0.0,0.0 4 | 2,hsa.miR.497.5p,0.0,0.179367,0.0,0.0,0.0,0.0,0.179367,0.0,0.0,0.0,0.0,0.0,0.0,0.23095,0.0,0.0,0.179367,0.23095,0.0,0.0 5 | 3,hsa.miR.17.5p,0.23095,0.0,0.0,0.0,0.0,0.179367,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.179367,0.0,0.23095,0.0,0.0,0.0,0.179367 6 | 4,hsa.miR.223.3p,0.0,0.142857,0.0,0.0,0.142857,0.0,0.0,0.0,0.142857,0.0,0.0,0.0,0.142857,0.142857,0.0,0.0,0.0,0.142857,0.0,0.142857 7 | 5,hsa.miR.29b.3p,0.0,0.0,0.0,0.0,0.0,0.0,0.234639,0.0,0.19134,0.19134,0.0,0.0,0.0,0.0,0.0,0.19134,0.0,0.19134,0.0,0.0 8 | 6,hsa.miR.301a.3p,0.0,0.142857,0.0,0.0,0.0,0.0,0.0,0.142857,0.142857,0.0,0.0,0.142857,0.0,0.142857,0.0,0.142857,0.0,0.142857,0.0,0.0 9 | 7,hsa.miR.29b.3p,0.0,0.0,0.0,0.0,0.0,0.0,0.234639,0.0,0.19134,0.19134,0.0,0.0,0.0,0.0,0.0,0.19134,0.0,0.19134,0.0,0.0 10 | 8,hsa.miR.139.5p,0.0,0.0,0.0,0.0,0.0,0.0,0.179367,0.0,0.0,0.0,0.0,0.0,0.179367,0.0,0.0,0.23095,0.179367,0.23095,0.0,0.0 11 | 9,hsa.miR.106a.5p,0.23095,0.0,0.0,0.0,0.0,0.179367,0.0,0.0,0.179367,0.0,0.0,0.0,0.0,0.0,0.0,0.23095,0.0,0.0,0.0,0.179367 12 | 10,hsa.miR.20b.5p,0.23095,0.0,0.0,0.0,0.0,0.179367,0.179367,0.0,0.0,0.0,0.0,0.0,0.0,0.179367,0.0,0.23095,0.0,0.0,0.0,0.0 13 | 11,hsa.miR.876.5p,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.234639,0.0,0.19134,0.0,0.0,0.0,0.0,0.0,0.19134,0.19134,0.0,0.19134,0.0 14 | 12,hsa.miR.544a,0.0,0.0,0.0,0.0,0.166667,0.0,0.166667,0.166667,0.0,0.166667,0.0,0.0,0.0,0.166667,0.0,0.0,0.0,0.166667,0.0,0.0 15 | 13,hsa.miR.24.3p,0.159044,0.0,0.0,0.0,0.0,0.159044,0.0,0.0,0.0,0.159044,0.0,0.0,0.0,0.0,0.0,0.204782,0.159044,0.0,0.159044,0.0 16 | 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12 | 10,hsa.miR.20b.5p,-28.535811,-28.537546,0.999939,-20.882032,-20.817512,1.003099,-2.4,0.090909 13 | 11,hsa.miR.876.5p,-29.855469,-29.798833,1.001901,-21.713801,-21.65482,1.002724,-1.7,0.095238 14 | 12,hsa.miR.544a,-30.745915,-30.7434,1.000082,-22.42795,-22.37183,1.002509,-1.5,0.095238 15 | 13,hsa.miR.24.3p,-30.256838,-30.240024,1.000556,-21.749422,-21.71527,1.001573,-2.7,0.095238 16 | 14,hsa.miR.3619.5p,-30.476559,-30.532825,0.998157,-22.068791,-22.094536,0.998835,-5.2,0.047619 17 | 15,hsa.miR.148b.3p,-29.555019,-29.55621,0.99996,-21.812316,-21.761315,1.002344,-0.7,0.142857 18 | 16,hsa.miR.199b.5p,-29.199445,-29.141611,1.001985,-20.501244,-20.414658,1.004241,-0.7,0.090909 19 | 17,hsa.miR.29b.3p,-28.986313,-28.994927,0.999703,-20.98151,-20.911544,1.003346,-1.4,0.090909 20 | 18,hsa.miR.26b.5p,-34.563517,-34.554448,1.000262,-23.598616,-23.462972,1.005781,0.0,0.0 21 | 19,hsa.miR.544a,-30.745915,-30.7434,1.000082,-22.42795,-22.37183,1.002509,-1.5,0.095238 22 | 20,hsa.miR.450a.5p,-32.744385,-32.735793,1.000262,-21.954965,-21.872578,1.003767,0.0,0.0 23 | 21,hsa.miR.429,-30.248755,-30.283626,0.998849,-21.78165,-21.725222,1.002597,-1.3,0.095238 24 | 22,hsa.miR.122.5p,-30.270283,-30.221411,1.001617,-21.488515,-21.45258,1.001675,-0.3,0.095238 25 | 23,hsa.miR.302a.3p,-29.226503,-29.218528,1.000273,-20.305142,-20.247291,1.002857,-1.6,0.090909 26 | 24,hsa.miR.448,-31.259298,-31.280275,0.999329,-21.861762,-21.813573,1.002209,-0.6,0.095238 27 | 25,hsa.miR.490.3p,-30.489055,-30.460683,1.000931,-21.634297,-21.600174,1.00158,-3.0,0.095238 28 | 26,hsa.miR.302d.3p,-28.968262,-28.938082,1.001043,-20.643832,-20.580257,1.003089,-0.7,0.090909 29 | 27,hsa.miR.149.5p,-29.118991,-29.106277,1.000437,-20.497477,-20.484172,1.00065,-1.7,0.090909 30 | 28,hsa.miR.491.5p,-29.651313,-29.656419,0.999828,-22.219316,-22.221451,0.999904,-3.6,0.095238 31 | 29,hsa.miR.155.5p,-27.674924,-27.641862,1.001196,-19.117074,-19.047137,1.003672,-0.4,0.086957 32 | 30,hsa.miR.122.5p,-30.270283,-30.221411,1.001617,-21.488515,-21.45258,1.001675,-0.3,0.095238 33 | 31,hsa.miR.302a.3p,-29.226503,-29.218528,1.000273,-20.305142,-20.247291,1.002857,-1.6,0.090909 34 | 32,hsa.miR.302a.3p,-29.226503,-29.218528,1.000273,-20.305142,-20.247291,1.002857,-1.6,0.090909 35 | 33,hsa.miR.302d.3p,-28.968262,-28.938082,1.001043,-20.643832,-20.580257,1.003089,-0.7,0.090909 36 | 34,hsa.miR.505.3p,-32.744385,-32.735793,1.000262,-21.649236,-21.544101,1.00488,0.0,0.0 37 | 35,hsa.miR.302d.3p,-28.968262,-28.938082,1.001043,-20.643832,-20.580257,1.003089,-0.7,0.090909 38 | 36,hsa.miR.149.5p,-29.118991,-29.106277,1.000437,-20.497477,-20.484172,1.00065,-1.7,0.090909 39 | 37,hsa.miR.496,-32.744385,-32.735793,1.000262,-21.829767,-21.710775,1.005481,0.0,0.0 40 | 38,hsa.miR.192.5p,-34.563517,-34.554448,1.000262,-23.699591,-23.622735,1.003253,0.0,0.0 41 | 39,hsa.miR.491.5p,-29.651313,-29.656419,0.999828,-22.219316,-22.221451,0.999904,-3.6,0.095238 42 | 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57 | 55,2TOB,224.7,5.275022,0.55,236.2886,1.660807 58 | 56,2OGN,80.814286,11.429487,-0.172857,7833.0996,2.83654 59 | 57,1XBP,80.814286,11.429487,-0.172857,7833.0996,2.83654 60 | 58,1F27,0.0,0.0,0.0,0.0,0.0 61 | 59,2FD0,0.0,0.0,0.0,0.0,0.0 62 | 60,1NEM,0.0,0.0,0.0,0.0,0.0 63 | 61,1AM0,0.0,0.0,0.0,0.0,0.0 64 | 62,2G9C,24.74,10.859909,0.393333,1705.0998,2.198681 65 | 63,2TOB,224.7,5.275022,0.55,236.2886,1.660807 66 | 64,1AM0,0.0,0.0,0.0,0.0,0.0 67 | 65,2ESJ,0.0,0.0,0.0,0.0,0.0 68 | 66,2F4U,0.0,0.0,0.0,0.0,0.0 69 | 67,1F27,0.0,0.0,0.0,0.0,0.0 70 | 68,2GIS,25.96875,11.105404,-1.6625,2048.4405,2.268237 71 | 69,2ET8,0.0,0.0,0.0,0.0,0.0 72 | 70,1TOB,0.0,0.0,0.0,0.0,0.0 73 | 71,1Y27,40.526667,11.999968,0.166667,1788.1668,2.176133 74 | 72,1O15,0.0,0.0,0.0,0.0,0.0 75 | 73,2FCZ,0.0,0.0,0.0,0.0,0.0 76 | 74,1FYP,0.0,0.0,0.0,0.0,0.0 77 | 75,1NEM,0.0,0.0,0.0,0.0,0.0 78 | 76,1HNW,0.0,0.0,0.0,0.0,0.0 79 | 77,1Y26,18.933333,5.753209,0.291667,1462.7139,2.406954 80 | 78,2O3X,0.0,0.0,0.0,0.0,0.0 81 | 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10,gi|1000814511|ref|NM_001320453.1|,0.7963,7.0,1.046595,37.0,0.827668 13 | 11,gi|1001184398|ref|NM_001320455.1|,0.4982,8.0,1.206993,7.0,0.159787 14 | 12,gi|1002623418|ref|NM_001320679.1|,0.4786,43.0,5.303193,208.0,3.165044 15 | 13,gi|1006456381|ref|NM_001321205.1|,0.478,20.0,2.722566,25.0,0.462947 16 | 14,gi|1007378466|ref|NM_001321202.1|,0.5018,18.0,2.477248,21.0,0.397726 17 | 15,gi|1010221562|ref|NM_001321553.1|,0.3868,17.0,2.653398,100.0,2.435473 18 | 16,gi|1010223708|ref|NM_001321552.1|,0.5131,13.0,2.061439,57.0,1.432704 19 | 17,gi|1012282594|ref|NM_001321706.1|,0.6162,4.0,0.630879,1.0,0.024889 20 | 18,gi|1013071015|ref|NM_001025591.3|,0.4983,35.0,4.32677,27.0,0.412839 21 | 19,gi|1013071031|ref|NM_001321918.1|,0.3797,37.0,4.920059,169.0,2.987935 22 | -------------------------------------------------------------------------------- /out/RNAonly/encoding_features/Codon related (1D).npy: -------------------------------------------------------------------------------- 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1,ENST00000332881.3,1.508923,22.43712,0.067251,6.255688,6.255688,6.255688,6.255688,6.255688 4 | 2,ENST00000333139.3,1.333249,36.59457,0.036433,12.012682,12.012682,12.012682,12.012682,12.012682 5 | 3,ENST00000354376.3,2.194224,35.839118,0.061224,16.102756,16.102756,16.102756,16.102756,16.102756 6 | 4,ENST00000360656.2,0.732674,8.649255,0.08471,2.234006,2.234006,2.234006,2.234006,2.234006 7 | 5,ENST00000364140.1,0.458411,4.68206,0.097908,0.92953,0.92953,0.92953,0.92953,0.92953 8 | 6,ENST00000366188.2,0.432034,5.97449,0.072313,1.299092,1.299092,1.299092,1.299092,1.299092 9 | 7,ENST00000366424.2,3.310031,23.608566,0.140205,7.518889,7.518889,7.518889,7.518889,7.518889 10 | 8,ENST00000367276.8,1.055365,10.589563,0.099661,2.804822,2.804822,2.804822,2.804822,2.804822 11 | 9,ENST00000367563.7,1.222076,10.585299,0.11545,1.991232,1.991232,1.991232,1.991232,1.991232 12 | 10,gi|1000814511|ref|NM_001320453.1|,0.947926,11.680342,0.081156,2.650023,2.650023,2.650023,2.650023,2.650023 13 | 11,gi|1001184398|ref|NM_001320455.1|,0.833376,10.716863,0.077763,3.11431,3.11431,3.11431,3.11431,3.11431 14 | 12,gi|1002623418|ref|NM_001320679.1|,3.005181,48.800376,0.061581,41.533465,41.533465,41.533465,41.533465,41.533465 15 | 13,gi|1006456381|ref|NM_001321205.1|,1.743552,22.29977,0.078187,4.686914,4.686914,4.686914,4.686914,4.686914 16 | 14,gi|1007378466|ref|NM_001321202.1|,1.086567,20.546396,0.052884,4.455812,4.455812,4.455812,4.455812,4.455812 17 | 15,gi|1010221562|ref|NM_001321553.1|,0.80826,9.021465,0.089593,1.394574,1.394574,1.394574,1.394574,1.394574 18 | 16,gi|1010223708|ref|NM_001321552.1|,0.62892,7.893756,0.079673,1.960473,1.960473,1.960473,1.960473,1.960473 19 | 17,gi|1012282594|ref|NM_001321706.1|,0.468118,7.909886,0.059181,2.800812,2.800812,2.800812,2.800812,2.800812 20 | 18,gi|1013071015|ref|NM_001025591.3|,9.112985,47.701641,0.191041,39.753731,39.753731,39.753731,39.753731,39.753731 21 | 19,gi|1013071031|ref|NM_001321918.1|,0.798213,27.682015,0.028835,15.061548,15.061548,15.061548,15.061548,15.061548 22 | -------------------------------------------------------------------------------- /out/RNAonly/encoding_features/EIIP based spectrum (1D).npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idrblab/rnaincoder/9a9db569eb359db493eddf9ba86d5e7a3b9050ef/out/RNAonly/encoding_features/EIIP based spectrum (1D).npy -------------------------------------------------------------------------------- /out/RNAonly/encoding_features/Entropy density of transcript (1D).csv: -------------------------------------------------------------------------------- 1 | ,Seqname,TraEA: Entropy density A on transcript,TraEC: Entropy density C on transcript,TraED: Entropy density D on transcript,TraEE: Entropy density E on transcript,TraEF: Entropy density F on transcript,TraEG: Entropy density G on transcript,TraEH: Entropy density H on transcript,TraEI: Entropy density I on transcript,TraEK: Entropy density K on transcript,TraEL: Entropy density L on transcript,TraEM: Entropy density M on transcript,TraEN: Entropy density N on transcript,TraEP: Entropy density P on transcript,TraEQ: Entropy density Q on transcript,TraER: Entropy density R on transcript,TraES: Entropy density S on transcript,TraET: Entropy density T on transcript,TraEV: Entropy density V on transcript,TraEW: Entropy density W on transcript,TraEY: Entropy density Y on transcript 2 | 0,ENST00000329743.3,0.096688,0.036067,0.044268,0.044268,0.026738,0.089019,0.026738,0.044268,0.058322,0.100157,0.015671,0.036067,0.080238,0.026738,0.080238,0.064458,0.044268,0.070119,0.0,0.015671 3 | 1,ENST00000332881.3,0.042398,0.035047,0.028934,0.047433,0.056528,0.049033,0.038823,0.061993,0.075083,0.091881,0.019668,0.067055,0.053626,0.044117,0.057935,0.079254,0.059314,0.040634,0.024491,0.026755 4 | 2,ENST00000333139.3,0.058587,0.056831,0.036375,0.037553,0.035175,0.052243,0.035175,0.045281,0.051289,0.09877,0.011707,0.039851,0.090461,0.043159,0.055937,0.089928,0.061142,0.051289,0.033953,0.015296 5 | 3,ENST00000354376.3,0.080966,0.06113,0.026145,0.042284,0.032373,0.087168,0.04125,0.027442,0.029956,0.08037,0.014507,0.019183,0.085537,0.045296,0.089275,0.082719,0.050052,0.060335,0.031176,0.012834 6 | 4,ENST00000360656.2,0.057629,0.033353,0.038038,0.046538,0.080686,0.08307,0.028303,0.033353,0.050431,0.067216,0.0,0.028303,0.075626,0.038038,0.08757,0.064164,0.067216,0.054121,0.038038,0.028303 7 | 5,ENST00000364140.1,0.074505,0.035941,0.044044,0.026693,0.026693,0.069402,0.044044,0.044044,0.057868,0.079233,0.015682,0.035941,0.057868,0.044044,0.079233,0.083624,0.063877,0.063877,0.026693,0.026693 8 | 6,ENST00000366188.2,0.05379,0.029687,0.04852,0.042812,0.042812,0.067535,0.05379,0.042812,0.029687,0.075332,0.029687,0.042812,0.078894,0.05379,0.071552,0.078894,0.042812,0.036579,0.029687,0.04852 9 | 7,ENST00000366424.2,0.064569,0.042194,0.04814,0.052288,0.037369,0.078702,0.058699,0.042194,0.04955,0.08791,0.017947,0.020216,0.062281,0.04814,0.065685,0.074001,0.059914,0.04814,0.026497,0.015565 10 | 8,ENST00000367276.8,0.101851,0.044746,0.051338,0.037473,0.037473,0.05442,0.01451,0.048118,0.051338,0.083587,0.01451,0.024811,0.092669,0.033524,0.075191,0.057376,0.057376,0.044746,0.037473,0.037473 11 | 9,ENST00000367563.7,0.043176,0.039762,0.028303,0.049529,0.043176,0.078646,0.039762,0.060707,0.070299,0.074613,0.032357,0.049529,0.060707,0.043176,0.068029,0.070299,0.052498,0.043176,0.028303,0.023953 12 | 10,gi|1000814511|ref|NM_001320453.1|,0.05654,0.013457,0.045037,0.053833,0.05102,0.07304,0.045037,0.045037,0.070911,0.097019,0.023081,0.034977,0.064093,0.053833,0.048091,0.089552,0.059148,0.045037,0.031259,0.0 13 | 11,gi|1001184398|ref|NM_001320455.1|,0.084458,0.024403,0.040568,0.056547,0.036885,0.082535,0.044064,0.040568,0.040568,0.076384,0.00816,0.028846,0.078501,0.044064,0.074196,0.094822,0.047395,0.040568,0.036885,0.019584 14 | 12,gi|1002623418|ref|NM_001320679.1|,0.072406,0.045239,0.02798,0.046672,0.058391,0.066831,0.033397,0.051467,0.057789,0.089248,0.01988,0.039972,0.064681,0.039972,0.057789,0.071427,0.049453,0.045959,0.023058,0.038388 15 | 13,gi|1006456381|ref|NM_001321205.1|,0.069135,0.042273,0.042273,0.040613,0.05429,0.068014,0.033527,0.040613,0.042273,0.086505,0.025555,0.031628,0.066875,0.047026,0.064536,0.086505,0.055657,0.052897,0.033527,0.016278 16 | 14,gi|1007378466|ref|NM_001321202.1|,0.076012,0.041229,0.041229,0.046451,0.061479,0.069142,0.037512,0.033574,0.043014,0.085074,0.027169,0.031511,0.048108,0.065419,0.070339,0.085074,0.037512,0.048108,0.024874,0.027169 17 | 15,gi|1010221562|ref|NM_001321553.1|,0.051844,0.029233,0.034412,0.034412,0.059151,0.047882,0.023573,0.074594,0.059151,0.089193,0.017263,0.047882,0.043681,0.051844,0.059151,0.087004,0.051844,0.055593,0.034412,0.047882 18 | 16,gi|1010223708|ref|NM_001321552.1|,0.07035,0.018721,0.010823,0.042257,0.042257,0.076644,0.031593,0.063404,0.073573,0.085049,0.010823,0.037137,0.063404,0.042257,0.079575,0.073573,0.047023,0.042257,0.042257,0.047023 19 | 17,gi|1012282594|ref|NM_001321706.1|,0.054648,0.046044,0.036273,0.054648,0.036273,0.100408,0.030815,0.0,0.081469,0.081469,0.024848,0.036273,0.094018,0.036273,0.078629,0.075662,0.036273,0.054648,0.041327,0.0 20 | 18,gi|1013071015|ref|NM_001025591.3|,0.047113,0.049225,0.03795,0.038763,0.03795,0.066334,0.047113,0.047113,0.046395,0.079496,0.029209,0.03014,0.080369,0.055833,0.066873,0.085743,0.048528,0.050597,0.03196,0.023297 21 | 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-------------------------------------------------------------------------------- /out/RNAonly/encoding_features/Guanine-cytosine related (1D).csv: -------------------------------------------------------------------------------- 1 | ,Seqname,GCCoW: GC content of whole sequence,GCCo1: GC content of 1st position of codons,GCCo2: GC content of 2nd position of codons,GCCo3: GC content of 3rd position of codons,GCC1V: GCCo1 variance frame score,GCC2V: GCCo2 variance frame score,GCC3V: GCCo3 variance frame score 2 | 0,ENST00000329743.3,0.60767,0.663717,0.530973,0.628319,0.014055,0.013493,0.014377 3 | 1,ENST00000332881.3,0.38664,0.374494,0.38664,0.398785,0.000462,0.000434,0.000436 4 | 2,ENST00000333139.3,0.497326,0.482517,0.526944,0.482517,0.001975,0.002003,0.00206 5 | 3,ENST00000354376.3,0.63647,0.615863,0.634526,0.65902,0.001439,0.001466,0.001467 6 | 4,ENST00000360656.2,0.525084,0.541806,0.546823,0.486622,0.003221,0.003106,0.002946 7 | 5,ENST00000364140.1,0.535385,0.507692,0.526154,0.572308,0.00368,0.003265,0.003408 8 | 6,ENST00000366188.2,0.5,0.541463,0.482927,0.47561,0.003681,0.004159,0.004362 9 | 7,ENST00000366424.2,0.523461,0.555759,0.502742,0.511883,0.002369,0.002465,0.002405 10 | 8,ENST00000367276.8,0.563686,0.573171,0.569106,0.54878,0.00046,0.000416,0.000386 11 | 9,ENST00000367563.7,0.454054,0.425676,0.45,0.486486,0.002933,0.003133,0.00311 12 | 10,gi|1000814511|ref|NM_001320453.1|,0.513716,0.508728,0.448878,0.583541,0.013855,0.013855,0.014223 13 | 11,gi|1001184398|ref|NM_001320455.1|,0.57351,0.572185,0.584106,0.564238,0.000285,0.000275,0.000228 14 | 12,gi|1002623418|ref|NM_001320679.1|,0.468534,0.482385,0.463415,0.459801,0.000432,0.000413,0.000407 15 | 13,gi|1006456381|ref|NM_001321205.1|,0.508715,0.49193,0.519045,0.515171,0.000669,0.00062,0.00065 16 | 14,gi|1007378466|ref|NM_001321202.1|,0.50979,0.516084,0.482517,0.530769,0.001855,0.001873,0.001787 17 | 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isoelectric point,ProAH: Pseudo protein average hydropathy,ProMW: Pseudo protein molecular weight,PPMFS: Pseudo protein PI-MW frame score 2 | 0,ENST00000329743.3,53.258065,9.640941,-0.264516,9592.9456,2.998269 3 | 1,ENST00000332881.3,53.449153,7.83776,-0.864407,6472.2675,2.91739 4 | 2,ENST00000333139.3,82.067729,9.564481,-0.201195,27886.3128,3.464879 5 | 3,ENST00000354376.3,85.041379,11.658027,-0.263054,22153.6447,3.279049 6 | 4,ENST00000360656.2,46.867925,10.029363,-0.573585,5898.6972,2.770221 7 | 5,ENST00000364140.1,65.033898,7.792052,-0.091525,6380.3107,2.91372 8 | 6,ENST00000366188.2,89.907317,6.522524,-0.217073,4996.8738,2.884849 9 | 7,ENST00000366424.2,105.688393,11.356896,-0.422321,12249.148,3.033249 10 | 8,ENST00000367276.8,26.352,9.100244,-0.676,3259.74,2.555341 11 | 9,ENST00000367563.7,46.191111,6.815075,-0.375556,10266.546,3.178242 12 | 10,gi|1000814511|ref|NM_001320453.1|,58.791667,6.526105,0.008333,8013.0349,3.089497 13 | 11,gi|1001184398|ref|NM_001320455.1|,62.117978,7.755476,-0.11236,9149.1295,3.072139 14 | 12,gi|1002623418|ref|NM_001320679.1|,72.367972,11.339296,-0.334164,30641.2307,3.431881 15 | 13,gi|1006456381|ref|NM_001321205.1|,74.913699,6.143408,0.052055,8226.2996,3.127119 16 | 14,gi|1007378466|ref|NM_001321202.1|,74.913699,6.143408,0.052055,8226.2996,3.127119 17 | 15,gi|1010221562|ref|NM_001321553.1|,65.470103,5.632881,-0.171134,10952.4519,3.289004 18 | 16,gi|1010223708|ref|NM_001321552.1|,65.470103,5.632881,-0.171134,10952.4519,3.289004 19 | 17,gi|1012282594|ref|NM_001321706.1|,75.174528,10.302773,-1.10283,11892.7821,3.062705 20 | 18,gi|1013071015|ref|NM_001025591.3|,48.002083,4.574198,0.423958,10563.1201,3.363665 21 | 19,gi|1013071031|ref|NM_001321918.1|,44.719767,4.848389,-0.296512,10231.6939,3.324556 22 | -------------------------------------------------------------------------------- /out/RNAonly/encoding_features/Pseudo protein related (1D).npy: 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0,ENST00000329743.3,-0.695474,-0.762524,0.912069,-0.577617,-0.599939,0.962793,-137.8,0.109467 3 | 1,ENST00000332881.3,-0.081241,-0.082423,0.985658,-0.086348,-0.084426,1.022762,-353.9,0.105334 4 | 2,ENST00000333139.3,-0.065089,-0.070526,0.922911,-0.05486,-0.05491,0.999085,-725.2,0.109877 5 | 3,ENST00000354376.3,-0.047267,-0.060164,0.785644,-0.042969,-0.047124,0.911844,-1238.4,0.116686 6 | 4,ENST00000360656.2,-0.353893,-0.381758,0.927009,-0.239978,-0.25565,0.938698,-194.7,0.127303 7 | 5,ENST00000364140.1,-0.757139,-0.778312,0.972796,-0.561549,-0.566815,0.990709,-110.3,0.138889 8 | 6,ENST00000366188.2,-0.539406,-0.556767,0.968818,-0.36743,-0.370772,0.990985,-121.7,0.124694 9 | 7,ENST00000366424.2,-0.063869,-0.081662,0.782117,-0.071221,-0.075597,0.942113,-594.6,0.122561 10 | 8,ENST00000367276.8,-0.182245,-0.209911,0.868203,-0.193948,-0.203315,0.953926,-284.6,0.126187 11 | 9,ENST00000367563.7,-0.3005,-0.303499,0.990118,-0.232634,-0.225731,1.030584,-215.1,0.105548 12 | 10,gi|1000814511|ref|NM_001320453.1|,-0.259563,-0.271711,0.955288,-0.20395,-0.205275,0.993549,-259.9,0.113608 13 | 11,gi|1001184398|ref|NM_001320455.1|,-0.287632,-0.308692,0.931776,-0.191456,-0.197923,0.967327,-299.0,0.12069 14 | 12,gi|1002623418|ref|NM_001320679.1|,-0.017552,-0.024329,0.721449,-0.021422,-0.023441,0.913887,-1078.8,0.112651 15 | 13,gi|1006456381|ref|NM_001321205.1|,-0.067359,-0.079995,0.842045,-0.070287,-0.070798,0.992793,-555.1,0.114341 16 | 14,gi|1007378466|ref|NM_001321202.1|,-0.073113,-0.087159,0.838851,-0.075925,-0.075875,1.000656,-517.4,0.115465 17 | 15,gi|1010221562|ref|NM_001321553.1|,-0.296592,-0.298513,0.993565,-0.261175,-0.260366,1.003104,-147.2,0.104305 18 | 16,gi|1010223708|ref|NM_001321552.1|,-0.352865,-0.371955,0.948676,-0.234589,-0.245443,0.95578,-171.0,0.111722 19 | 17,gi|1012282594|ref|NM_001321706.1|,-0.341945,-0.393646,0.86866,-0.301339,-0.317296,0.949712,-205.2,0.100885 20 | 18,gi|1013071015|ref|NM_001025591.3|,-0.035404,-0.041598,0.8511,-0.035993,-0.037342,0.963878,-1092.7,0.110531 21 | 19,gi|1013071031|ref|NM_001321918.1|,-0.026093,-0.031745,0.821967,-0.057037,-0.056392,1.011432,-486.5,0.109061 22 | -------------------------------------------------------------------------------- /out/RNAonly/encoding_features/Secondary structure (1D).npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idrblab/rnaincoder/9a9db569eb359db493eddf9ba86d5e7a3b9050ef/out/RNAonly/encoding_features/Secondary structure (1D).npy -------------------------------------------------------------------------------- /out/RNAonly/encoding_features/Sequence-intrinsic Features_One-hot encoding (2D).npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idrblab/rnaincoder/9a9db569eb359db493eddf9ba86d5e7a3b9050ef/out/RNAonly/encoding_features/Sequence-intrinsic 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patsy>=0.5.1 10 | 11 | # Machine learning packages 12 | tensorflow>=2.4.1 13 | # tensorflow-gpu>=2.2.0 # Removed due to installation issues 14 | keras>=2.4.3 15 | xgboost>=1.4.2 16 | lightgbm>=3.2.1 17 | gensim>=3.8.3 18 | 19 | # Deep learning utilities 20 | tensorboard>=2.2.2 21 | tensorboardX>=2.4 22 | h5py>=2.10.0 23 | 24 | # Dimensionality reduction and clustering 25 | umap-learn>=0.5.1 26 | pca>=1.4.0 27 | 28 | # Bio-related packages 29 | biopython>=1.78 30 | CPAT>=3.0.2 31 | pysam>=0.16.0.1 32 | SimpleITK>=2.0.2 33 | 34 | # Feature selection and encoding 35 | category-encoders>=2.2.2 36 | mrmr_selection 37 | 38 | # Utilities 39 | tqdm>=4.60.0 40 | joblib>=1.0.1 41 | pyyaml>=5.4.1 42 | tabulate>=0.8.9 43 | wget>=3.2 44 | colored>=1.4.2 45 | colorlog>=6.5.0 46 | 47 | # Jupyter and interactive environment 48 | notebook>=6.4.0 49 | ipython>=7.22.0 50 | ipykernel>=5.3.4 51 | 52 | # Web and API packages 53 | requests>=2.25.1 54 | aiohttp>=3.7.4 55 | 56 | # Computation speedup 57 | numba>=0.53.0 58 | cython>=0.29.23 59 | 60 | # Visualization 61 | pygal>=2.4.0 62 | palettable>=3.3.0 63 | colourmap>=0.1.1 64 | -------------------------------------------------------------------------------- /rnaincoder.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env Python 2 | # coding=utf-8 3 | from utility import RNAcoding_01,model 4 | import argparse as agp 5 | 6 | 7 | def rnaincoder_process(type,Afastapath,Interfilepath,Resultpath,dimension,savetype,n_select,com_num,modelnm,Bfastapath=None): 8 | # calcuation =========================================== 9 | resultpath = Resultpath + '/' + type 10 | # encoding part 11 | if type =='RNAonly': 12 | RNAcoding_01.RNA_coding(Afastapath, Interfilepath, resultpath, dimension = dimension, savetype = savetype,n_select = n_select) 13 | 14 | elif type =='RNA-RNA': 15 | RNAcoding_01.RNA_RNA_coding(Afastapath,Bfastapath,Interfilepath,resultpath,dimension = dimension, savetype = savetype,n_select =n_select) 16 | 17 | elif type =='RNA-pro': 18 | RNAcoding_01.RNA_protein_coding(Afastapath,Bfastapath,Interfilepath,resultpath,dimension = dimension, savetype = savetype,n_select =n_select) 19 | 20 | elif type =='RNA-compound': 21 | RNAcoding_01.RNA_compound_coding(Afastapath,Bfastapath,Interfilepath,resultpath,dimension = dimension, savetype = savetype,n_select =n_select) 22 | # evaluation part 23 | datapath = Resultpath + '/' + type + '/' + 'encoding_features' 24 | if type =='RNAonly': 25 | model.evaluation_method(datapath,Interfilepath,resultpath,type = type,com_num = com_num,modelnm = modelnm) 26 | else: 27 | model.evaluation_interaction(datapath,Interfilepath,resultpath,type = type,com_num = com_num,modelnm = modelnm) 28 | 29 | def main(): 30 | # parameters =========================================== 31 | # encoding part 32 | Resultpath = './output' 33 | type = 'RNAonly' # RNAonly, RNA-RNA, RNA-pro, RNA-compound 34 | dimension = '2' # only type is RNAonly, RNA-RNA, RNA-pro, it is 2 35 | savetype = 'npycsv' 36 | n_select = None 37 | 38 | # evaluation part 39 | modelnm = 'DNN' # 'RF','svm','xgboost','DNN','CNN' 40 | com_num = 2 # number of combination methods 41 | # data part 42 | Afastapath = './demo/RNA-only/Homo38_small.fasta' 43 | Bfastapath = None 44 | Interfilepath = './demo/RNA-only/Homo38_small.csv' 45 | 46 | # Afastapath = './demo/RNA-RNA/SampleData-lncRNA-A.fasta' 47 | # Bfastapath = './demo/RNA-RNA/SampleData-miRNA-B.fasta' 48 | # Interfilepath = './demo/RNA-RNA/RNA-RNA-Interacting.csv' 49 | 50 | # Afastapath = './demo/RNA-Protein/SampleData-RNA-A.fasta' 51 | # Bfastapath = './demo/RNA-Protein/SampleData-Protein-B.fasta' 52 | # Interfilepath = './demo/RNA-Protein/RNA-Protein-Interacting.csv' 53 | 54 | # Afastapath = './demo/RNA-SamllMoleculer/SampleData-RNA-A.fasta' 55 | # Bfastapath = './demo/RNA-SamllMoleculer/Small-Moleculer.smi' 56 | # Interfilepath = './demo/RNA-SamllMoleculer/RNA-small-molecule-Interacting.csv' 57 | 58 | # 外部输入参数计算---------------------------- 59 | parser = agp.ArgumentParser() 60 | parser.add_argument('-t','--type',help="The encoding file type: RNAonly, RNA-RNA, RNA-pro, RNA-compound. It is the coding task of a single RNA fasta file, or RNA interaction task.") 61 | parser.add_argument('-a','--Afastapath',help="The RNA fasta A file path. RNA fasta format is necessary and standard fasta format can be seen https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp.") 62 | parser.add_argument('-b','--Bfastapath',default = None,help="The encoding fasta B file. If the type is RNAonly, this file is not necessary.") 63 | parser.add_argument('-l','--Interfilepath',help="The label file. This file format is .csv format.") 64 | parser.add_argument('-o','--Resultpath',help="The encoding result file path.") 65 | parser.add_argument('-d','--dimension',type = str,default = '1', help="The feature dimension of encoding feature: 1 or 2.") 66 | parser.add_argument('-s','--savetype', type = str,default = 'csvnpy',help="The encoding result file type: csvnpy or csv or npy, defatult is csv and npy.") 67 | parser.add_argument('-n','--n_select', type = int,default = None,help="The encoding feature number: 1-10. Default is all encoding features.") 68 | parser.add_argument('-c','--com_num', type = int,default = None,help="Number of combination features: 1-10. Default is all encoding features combinations (1023).") 69 | parser.add_argument('-m','--modelnm', type = str,default = 'RF',help="Classification model of evaluation feature combination:'RF','svm','xgboost','DNN','CNN'.") 70 | args = parser.parse_args() 71 | rnaincoder_process(args.type,args.Afastapath,args.Interfilepath,args.Resultpath,args.dimension,args.savetype,args.n_select,args.com_num,args.modelnm,args.Bfastapath) 72 | 73 | if __name__ == '__main__': 74 | main() 75 | --------------------------------------------------------------------------------