├── .project ├── .settings └── org.eclipse.core.resources.prefs ├── README.md ├── exercise01 ├── Theano을활용한딥러닝실습_01.ipynb ├── cancer_data_structur.ipynb ├── logisticRegression.py ├── mRNA_Upload_script.ipynb ├── mRNA_make_feature.ipynb └── tcga_mrna_down.jpg ├── main.jpg ├── main_02.jpg ├── main_03.jpg ├── main_04.jpg ├── part01 ├── Week1_151103 │ ├── BioPython과Theano설치.pptx │ └── BioPython과Theano설치.txt ├── Week1_151110 │ ├── 02장연습문제.ipynb │ └── DeepBio_Theano_sejinpark.ipynb ├── Week1_151117 │ ├── 5장연습문제.ipynb │ ├── chap06_study.ipynb │ ├── chap07_file_study.ipynb │ └── chap10_Tuple_study.ipynb └── Week1_151124 │ ├── Py4Inf-08-Lists.pptx │ ├── Py4Inf-09-Dictionaries.pptx │ └── chapter_09_dictionary_exercise.ipynb ├── part02 ├── Week1_151201 │ ├── 11장연습문제.ipynb │ ├── BeautifulSoup.py │ ├── Derivates in Theano.ipynb │ ├── Network.ipynb │ └── Regular expression.ipynb ├── Week2_151208 │ ├── Py4Inf-14-Database.ppt │ ├── Py4Inf-14-Databases.pptx │ ├── Py4Inf-15-Data-Viz.pptx │ ├── theano_05_configureation settings and compiling modes.ipynb │ └── theano_06_loading and saving.ipynb ├── Week3_151215 │ ├── Chapter1.Python_and_the_Surrounding_Software_Ecology.ipynb │ ├── Interfacing_R.ipynb │ ├── R_magic.ipynb │ ├── theano_loop_kang_ik_cho.ipynb │ └── theano_loop_kang_ik_cho.pdf └── Week4_151229 │ ├── Analyze_edited.ipy │ ├── analysis code.ipynb │ ├── biopython_ch02 │ ├── 01.Accessing_Databases.ipynb │ ├── 02.Basic_Sequence_Processing.ipynb │ ├── 03.Working_with_FASTQ.ipynb │ ├── 04.Working_with_BAM.ipynb │ ├── 05.Working_with_VCF.ipynb │ ├── 06.Filtering_SNPs.ipynb │ └── Chapter 2. Next-generation Sequencing.ipynb │ ├── paper_review │ ├── Analyze_edited.ipy │ ├── Assessing the clinical utility of cancer genomic and proteomic data across tumor types.ipynb │ ├── analysis code.ipynb │ └── figures │ │ ├── fig1.jpg │ │ ├── fig2.jpg │ │ ├── fig3.jpg │ │ ├── fig4.jpg │ │ ├── fig5.jpg │ │ ├── fig_hazard_survival.png │ │ ├── fig_mortality_ref.png │ │ ├── fig_survival.png │ │ ├── table1.png │ │ ├── table_dataset.png │ │ ├── test.png │ │ ├── tmp1.png │ │ ├── tmp2.png │ │ ├── tmp3.png │ │ └── tmp4.png │ └── theano_발표자료_sparse&GPU.pdf ├── part03 ├── Week1_160105 │ ├── 105cancer_genomics_studies요약정보.xlsx │ ├── Cancer_Data.ipynb │ ├── RNA-seq_data_analysis.ipynb │ ├── array_based_expression_data_01.jpg │ ├── biopython_ch03 │ │ ├── 01.Reference_Genome.ipynb │ │ ├── 02.Low_Quality.ipynb │ │ ├── 03.Annotations.ipynb │ │ ├── 04.Getting_Gene.ipynb │ │ ├── 05.Orthology.ipynb │ │ ├── 06.Gene_Ontology.ipynb │ │ ├── README.md │ │ ├── bioinfo-6-141007062607-conversion-gate01.pptx │ │ ├── example.png │ │ ├── falciparum.png │ │ └── graph.png │ ├── cBioPortal_WebInterface.xlsx │ ├── clinical_data_01.jpg │ ├── copy_number_data_01.jpg │ ├── dna_methylation_data_01.jpg │ ├── dns_seq_01.jpg │ └── proteinl_data_01.jpg ├── Week2_160112 │ └── biopython04 │ │ ├── README.md │ │ ├── biopython_04_population genetics1.ipynb │ │ ├── biopython_04_population genetics2.ipynb │ │ ├── biopython_04_population genetics3.ipynb │ │ ├── biopython_04_population genetics4.ipynb │ │ ├── biopython_04_population genetics5.ipynb │ │ └── biopython_04_population genetics6.ipynb ├── Week2_160119 │ ├── 04_PopSim │ │ ├── Basic_SimuPOP.ipynb │ │ ├── Coalescent.ipynb │ │ ├── Complex.ipynb │ │ ├── Pop_Structure.ipynb │ │ ├── README.md │ │ ├── Selection.ipynb │ │ ├── Untitled.ipynb │ │ ├── example.png │ │ ├── island_10_0.01_100_30.par │ │ └── tmp.par │ └── MLP │ │ ├── MLP_cede.ipynb │ │ ├── Untitled.ipynb │ │ ├── chap4.pdf │ │ ├── logistic_sgd.py │ │ ├── logistic_sgd.pyc │ │ ├── mlp.png │ │ ├── mlp.py │ │ ├── result │ │ └── untitled └── Week4_160126 │ ├── CNN 이론 II_Final.pptx │ ├── CNN 이론 I_Final.pptx │ ├── CNN 코드 in Theano_Final.pptx │ ├── Tensor 기초_Final.pptx │ └── Tensor 참고 자료.PDF ├── part04 ├── Week1_160202 │ ├── DenoisingAutoencoders.ipynb │ ├── biopython_pdb │ │ ├── 01.Intro.ipynb │ │ ├── 02.PDB.ipynb │ │ ├── 03.Stats.ipynb │ │ ├── 04.Distance.ipynb │ │ ├── 05.Mass.ipynb │ │ ├── 06.Parser.ipynb │ │ ├── 07.mmCIF.ipynb │ │ ├── PyMol_Intro.py │ │ ├── PyMol_Movie.py │ │ ├── README.md │ │ └── example.png │ └── dA_plots │ │ ├── filters_corruption_0.png │ │ └── filters_corruption_30.png └── Week3_160223 │ ├── DBN_test.html │ ├── RBM 이론_Final_Final.pptx │ └── fig │ ├── norm1.png │ ├── norm2.png │ ├── rbm_str.PNG │ └── structure.PNG └── reference ├── 00_cuda_install.ipynb ├── Basset.txt ├── pydot_error.txt └── theano_more_examples.ipynb /.project: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biospin/DeepBio/HEAD/.project 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