├── LICENSE.txt ├── README.md ├── datasets ├── clip │ ├── 10_PARCLIP_ELAVL1A_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 11_CLIPSEQ_ELAVL1_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 12_PARCLIP_EWSR1_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 13_PARCLIP_FUS_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 14_PARCLIP_FUS_mut_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 15_PARCLIP_IGF2BP123_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 16_ICLIP_hnRNPC_Hela_iCLIP_all_clusters │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 17_ICLIP_HNRNPC_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 18_ICLIP_hnRNPL_Hela_group_3975_all-hnRNPL-Hela-hg19_sum_G_hg19--ensembl59_from_2337-2339-741_bedGraph-cDNA-hits-in-genome │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 19_ICLIP_hnRNPL_U266_group_3986_all-hnRNPL-U266-hg19_sum_G_hg19--ensembl59_from_2485_bedGraph-cDNA-hits-in-genome │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 1_PARCLIP_AGO1234_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 20_ICLIP_hnRNPlike_U266_group_4000_all-hnRNPLlike-U266-hg19_sum_G_hg19--ensembl59_from_2342-2486_bedGraph-cDNA-hits-in-genome │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 21_PARCLIP_MOV10_Sievers_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 22_ICLIP_NSUN2_293_group_4007_all-NSUN2-293-hg19_sum_G_hg19--ensembl59_from_3137-3202_bedGraph-cDNA-hits-in-genome │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 23_PARCLIP_PUM2_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 24_PARCLIP_QKI_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 25_CLIPSEQ_SFRS1_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 26_PARCLIP_TAF15_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 27_ICLIP_TDP43_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 28_ICLIP_TIA1_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 29_ICLIP_TIAL1_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 2_PARCLIP_AGO2MNASE_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 30_ICLIP_U2AF65_Hela_iCLIP_ctrl_all_clusters │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 31_ICLIP_U2AF65_Hela_iCLIP_ctrl+kd_all_clusters │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 3_HITSCLIP_Ago2_binding_clusters │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 4_HITSCLIP_Ago2_binding_clusters_2 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 5_CLIPSEQ_AGO2_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 6_CLIP-seq-eIF4AIII_1 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 7_CLIP-seq-eIF4AIII_2 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ ├── 8_PARCLIP_ELAVL1_hg19 │ │ └── 5000 │ │ │ ├── test_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ │ │ └── training_sample_0 │ │ │ ├── matrix_Cobinding.tab.gz │ │ │ ├── matrix_GeneOntology.tab.gz │ │ │ ├── matrix_RNAfold.tab.gz │ │ │ ├── matrix_RNAkmers.tab.gz │ │ │ ├── matrix_RegionType.tab.gz │ │ │ ├── matrix_Response.tab.gz │ │ │ ├── positions.bedGraph.gz │ │ │ └── sequences.fa.gz │ └── 9_PARCLIP_ELAVL1MNASE_hg19 │ │ └── 5000 │ │ ├── test_sample_0 │ │ ├── matrix_Cobinding.tab.gz │ │ ├── matrix_GeneOntology.tab.gz │ │ ├── matrix_RNAfold.tab.gz │ │ ├── matrix_RNAkmers.tab.gz │ │ ├── matrix_RegionType.tab.gz │ │ ├── matrix_Response.tab.gz │ │ ├── positions.bedGraph.gz │ │ └── sequences.fa.gz │ │ └── training_sample_0 │ │ ├── matrix_Cobinding.tab.gz │ │ ├── matrix_GeneOntology.tab.gz │ │ ├── matrix_RNAfold.tab.gz │ │ ├── matrix_RNAkmers.tab.gz │ │ ├── matrix_RegionType.tab.gz │ │ ├── matrix_Response.tab.gz │ │ ├── positions.bedGraph.gz │ │ └── sequences.fa.gz └── yeast_rpr │ ├── yeast_rpr.txt │ ├── yeast_rpr_Xn.txt │ ├── yeast_rpr_Xp.txt │ ├── yeast_rpr_columns.txt │ ├── yeast_rpr_y0.txt │ ├── yeast_rpr_y1.txt │ └── yeast_rpr_y2.txt ├── examples ├── __init__.py ├── clip.py └── yeast_rpr.py ├── img ├── clip.png └── yeast_rpr.png ├── ionmf ├── __init__.py └── factorization │ ├── __init__.py │ ├── model.py │ └── onmf.py ├── requirements.txt ├── setup.cfg └── setup.py /LICENSE.txt: -------------------------------------------------------------------------------- 1 | Copyright (c) 2013 Laboratory of Bioinformatics, Faculty of Computer and 2 | Information Science, University of Ljubljana, Slovenia 3 | 4 | All rights reserved. 5 | 6 | Redistribution and use in source and binary forms, with or without 7 | modification, are permitted provided that the following conditions are met: 8 | 9 | 1. Redistributions of source code must retain the above copyright notice, this 10 | list of conditions and the following disclaimer. 11 | 2. Redistributions in binary form must reproduce the above copyright notice, 12 | this list of conditions and the following disclaimer in the documentation 13 | and/or other materials provided with the distribution. 14 | 15 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 16 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 17 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 18 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 19 | ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 20 | (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 21 | LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 22 | ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 23 | (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 24 | SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 25 | -------------------------------------------------------------------------------- /datasets/clip/10_PARCLIP_ELAVL1A_hg19/5000/test_sample_0/matrix_Cobinding.tab.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mstrazar/iONMF/a22c8654a147a929d2a4894fffb89d6b17b47f2f/datasets/clip/10_PARCLIP_ELAVL1A_hg19/5000/test_sample_0/matrix_Cobinding.tab.gz 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1.000000000000000000e+00 183 | 1.000000000000000000e+00 184 | 1.000000000000000000e+00 185 | 1.000000000000000000e+00 186 | 1.000000000000000000e+00 187 | -------------------------------------------------------------------------------- /examples/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mstrazar/iONMF/a22c8654a147a929d2a4894fffb89d6b17b47f2f/examples/__init__.py -------------------------------------------------------------------------------- /examples/yeast_rpr.py: -------------------------------------------------------------------------------- 1 | from ionmf.factorization.model import iONMF 2 | import matplotlib.pyplot as plt 3 | import numpy as np 4 | np.set_printoptions(precision=5) 5 | 6 | 7 | def load_data(): 8 | 9 | # Load data 10 | Xp = np.loadtxt(fname="../datasets/yeast_rpr/yeast_rpr_Xp.txt") # Features; Positive differential expression 11 | Xn = np.loadtxt(fname="../datasets/yeast_rpr/yeast_rpr_Xn.txt") # Features; Negative differential expression 12 | y0 = np.loadtxt(fname="../datasets/yeast_rpr/yeast_rpr_y0.txt") # Class 0 binary vector 13 | y1 = np.loadtxt(fname="../datasets/yeast_rpr/yeast_rpr_y1.txt") # Class 1 binary vector 14 | y2 = np.loadtxt(fname="../datasets/yeast_rpr/yeast_rpr_y2.txt") # Class 2 binary vector 15 | 16 | print Xp.shape 17 | print Xn.shape 18 | 19 | return { 20 | "Pos_diff_expr": Xp, 21 | "Neg_diff_expr": Xn, 22 | "Class_0": y0.reshape((len(y0), 1)), 23 | "Class_1": y1.reshape((len(y1), 1)), 24 | "Class_2": y2.reshape((len(y2), 1)), 25 | } 26 | 27 | 28 | 29 | def run(): 30 | 31 | datadict = load_data() 32 | model = iONMF(rank=5, max_iter=100, alpha=0.0) 33 | 34 | # Fit all training data 35 | model.fit(datadict) 36 | 37 | # Make predictions about class on all training data 38 | # using only expression data ... 39 | testdict = dict() 40 | testdict["Pos_diff_expr"] = datadict["Pos_diff_expr"] 41 | testdict["Neg_diff_expr"] = datadict["Neg_diff_expr"] 42 | rdict = model.predict(testdict) 43 | 44 | 45 | # ... and calculate training error 46 | true_y = np.zeros((len(datadict["Class_0"]), 1)) 47 | true_y[np.where(datadict["Class_0"])] = 0 48 | true_y[np.where(datadict["Class_1"])] = 1 49 | true_y[np.where(datadict["Class_2"])] = 2 50 | 51 | predictions = np.array([np.argmax([rdict["Class_0"][i], rdict["Class_1"][i], 52 | rdict["Class_2"][i]]) 53 | for i in xrange(len(true_y))]) 54 | 55 | acc = np.sum(predictions == true_y.ravel()) / float(len(true_y)) 56 | print "Training accuracy: ", acc 57 | 58 | # Plot matrices 59 | plt.figure(figsize=(12, 12)) 60 | for ki, ky in enumerate(testdict.keys()): 61 | plt.subplot(len(testdict), 2, 2*ki+1) 62 | plt.title(ky) 63 | plt.imshow(datadict[ky]) 64 | plt.subplot(len(testdict), 2, 2*ki+2) 65 | plt.title(ky + " (approx.)") 66 | plt.imshow(model.coef_.dot(model.basis_[ky])) 67 | plt.show() 68 | 69 | if __name__ == "__main__": 70 | run() 71 | 72 | -------------------------------------------------------------------------------- /img/clip.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mstrazar/iONMF/a22c8654a147a929d2a4894fffb89d6b17b47f2f/img/clip.png -------------------------------------------------------------------------------- /img/yeast_rpr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mstrazar/iONMF/a22c8654a147a929d2a4894fffb89d6b17b47f2f/img/yeast_rpr.png -------------------------------------------------------------------------------- /ionmf/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /ionmf/factorization/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /ionmf/factorization/onmf.py: -------------------------------------------------------------------------------- 1 | from numpy.random import rand 2 | from numpy import nan_to_num 3 | 4 | def onmf(X, rank, alpha=1.0, max_iter=100, H_init=None, W_init=None): 5 | """ 6 | Orthogonal non-negative matrix factorization. 7 | 8 | Parameters 9 | ---------- 10 | X: array [m x n] 11 | Data matrix. 12 | rank: int 13 | Maximum rank of the factor model. 14 | alpha: int 15 | Orthogonality regularization parameter. 16 | max_iter: int 17 | Maximum number of iterations. 18 | H_init: array [rank x n] 19 | Fixed initial basis matrix. 20 | W_init: array [m x rank] 21 | Fixed initial coefficient matrix. 22 | 23 | Returns 24 | W: array [m x rank] 25 | Coefficient matrix (row clustering). 26 | H: array [rank x n] 27 | Basis matrix (column clustering / patterns). 28 | """ 29 | 30 | m, n = X.shape 31 | W = rand(m, rank) if isinstance(W_init, type(None)) else W_init 32 | H = rand(rank, n) if isinstance(H_init, type(None)) else H_init 33 | 34 | for itr in xrange(max_iter): 35 | if isinstance(W_init, type(None)): 36 | enum = X.dot(H.T) 37 | denom = W.dot(H.dot(H.T)) 38 | W = nan_to_num(W * enum/denom) 39 | 40 | if isinstance(H_init, type(None)): 41 | HHTH = H.dot(H.T).dot(H) 42 | enum = W.T.dot(X) + alpha * H 43 | denom = W.T.dot(W).dot(H) + 2.0 * alpha * HHTH 44 | H = nan_to_num(H * enum / denom) 45 | 46 | 47 | return W, H 48 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | numpy>=1.9.0 2 | sklearn>=0.14.0 3 | matplotlib>=1.4.3 4 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [metadata] 2 | description-file = README.md 3 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from distutils.core import setup 2 | setup( 3 | name = 'ionmf', 4 | packages = ['ionmf', 'ionmf.factorization'], 5 | version = '1.1', 6 | description = 'Integrative orthogonal non-negative matrix factorization with examples.', 7 | author = 'Martin Strazar', 8 | author_email = 'martin.strazar@gmail.com', 9 | url = 'https://github.com/mstrazar/iONMF', 10 | download_url = 'https://github.com/mstrazar/iONMF/tarball/1.1', 11 | keywords = ['data integration', 'matrix factorization', 'machine learning'], 12 | classifiers = [], 13 | ) 14 | --------------------------------------------------------------------------------