# Bioinformatics Tutorial

## Bioinformatics Tutorial

- [Bioinformatics Tutorial](https://book.ncrnalab.org/teaching/readme.md): 《生物信息学实践教程》
- [Getting Started](https://book.ncrnalab.org/teaching/getting-started.md)
- [Setup](https://book.ncrnalab.org/teaching/getting-started/setup.md): 工欲善其事，必先利其器
- [Run jobs in a Docker](https://book.ncrnalab.org/teaching/getting-started/docker.md)
- [Run jobs in a cluster \[Advanced\]](https://book.ncrnalab.org/teaching/getting-started/cluster.md)
- [Run GPU jobs \[Advanced\]](https://book.ncrnalab.org/teaching/getting-started/run-gpu-jobs-advanced.md)
- [1.Linux](https://book.ncrnalab.org/teaching/part-i.-programming-skills/1.linux.md)
- [1.1.Basic Command](https://book.ncrnalab.org/teaching/part-i.-programming-skills/1.linux/1.1.linux-basic-command.md)
- [1.2.Practice Guide](https://book.ncrnalab.org/teaching/part-i.-programming-skills/1.linux/1.2.linux-practice-guide.md)
- [1.3.Linux Bash](https://book.ncrnalab.org/teaching/part-i.-programming-skills/1.linux/1.3.linux-bash.md)
- [2.R](https://book.ncrnalab.org/teaching/part-i.-programming-skills/2.r.md)
- [2.1.R Basics](https://book.ncrnalab.org/teaching/part-i.-programming-skills/2.r/2.1.r-basics.md)
- [2.2.Plot with R](https://book.ncrnalab.org/teaching/part-i.-programming-skills/2.r/2.2.plots-with-r.md)
- [3.Python](https://book.ncrnalab.org/teaching/part-i.-programming-skills/3.python.md)
- [1.Blast](https://book.ncrnalab.org/teaching/part-ii.-basic-analyses/1.seqblast.md)
- [2.Conservation Analysis](https://book.ncrnalab.org/teaching/part-ii.-basic-analyses/2.conservation-analysis.md)
- [3.Function Analysis](https://book.ncrnalab.org/teaching/part-ii.-basic-analyses/3.function-analysis.md)
- [3.1.GO](https://book.ncrnalab.org/teaching/part-ii.-basic-analyses/3.function-analysis/3.1.go.md)
- [3.2.KEGG](https://book.ncrnalab.org/teaching/part-ii.-basic-analyses/3.function-analysis/3.2.kegg.md)
- [3.3.GSEA](https://book.ncrnalab.org/teaching/part-ii.-basic-analyses/3.function-analysis/3.3.gsea.md)
- [4.Clinical Analyses](https://book.ncrnalab.org/teaching/part-ii.-basic-analyses/4.clinical-analyses.md)
- [4.1.Survival Analysis](https://book.ncrnalab.org/teaching/part-ii.-basic-analyses/4.clinical-analyses/survival_analysis.md)
- [1.Mapping](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/1.mapping.md)
- [1.1 Genome Browser](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/1.mapping/1.1-genome-browser.md)
- [1.2 bedtools and samtools](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/1.mapping/1.2-bedtools-samtools.md)
- [2.RNA-seq](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/2.rna-seq.md)
- [2.1.Expression Matrix](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/2.rna-seq/2.1.expression-matrix.md)
- [2.2.Differential Expression with Cufflinks](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/2.rna-seq/2.2.differential-expression-with-cufflinks.md)
- [2.3.Differential Expression with DEseq2 and edgeR](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/2.rna-seq/2.3.differential_expression_with_deseq2-edger.md)
- [3.ChIP-seq](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/3.chip-seq.md)
- [4.Motif](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/4.motif.md)
- [4.1.Sequence Motif](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/4.motif/sequence_motif.md)
- [4.2.Structure Motif](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/4.motif/structure_motif.md)
- [5.RNA Network](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/5.rna-network.md)
- [5.1.Co-expression Network](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/5.rna-network/co_expression.md)
- [5.2.miRNA Targets](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/5.rna-network/mirna-targets.md)
- [5.3. CLIP-seq (RNA-Protein Interaction)](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/5.rna-network/clip-seq.md)
- [6.RNA Regulation - I](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation.md)
- [6.1.Alternative Splicing](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation/alternative-splicing.md)
- [6.2.APA (Alternative Polyadenylation)](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation/apa.md)
- [6.3.Chimeric RNA](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation/chimeric.md)
- [6.4.RNA Editing](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation/rna_editing.md)
- [6.5.SNV/INDEL](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/6.rna-regulation/snv_rna-seq.md)
- [7.RNA Regulation - II](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/7.rna-regulation-ii.md)
- [7.1.Translation: Ribo-seq](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/7.rna-regulation-ii/ribo_seq.md)
- [7.2.RNA Structure](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/7.rna-regulation-ii/structure.md)
- [8.cfDNA](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/8.cfdna.md)
- [8.1.Basic cfDNA-seq Analyses](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/8.cfdna/8.1.basic-cfdna-seq-analyses.md)
- [1.Machine Learning Basics](https://book.ncrnalab.org/teaching/part-iv.-machine-learning/1.machine-learning-basics.md)
- [1.1 Data Pre-processing](https://book.ncrnalab.org/teaching/part-iv.-machine-learning/1.machine-learning-basics/1.1.data-preprocessing.md)
- [1.2 Data Visualization & Dimension Reduction](https://book.ncrnalab.org/teaching/part-iv.-machine-learning/1.machine-learning-basics/1.2.data-dimension-reduction.md)
- [1.3 Feature Extraction and Selection](https://book.ncrnalab.org/teaching/part-iv.-machine-learning/1.machine-learning-basics/1.3.feature-engineering.md)
- [1.4 Machine Learning Classifiers/Models](https://book.ncrnalab.org/teaching/part-iv.-machine-learning/1.machine-learning-basics/1.4.machine-learning-model.md)
- [1.5 Performance Evaluation](https://book.ncrnalab.org/teaching/part-iv.-machine-learning/1.machine-learning-basics/1.5.model-evaluation.md)
- [2.Machine Learning with R](https://book.ncrnalab.org/teaching/part-iv.-machine-learning/2.machine-learning-with-r.md)
- [3.Machine Learning with Python](https://book.ncrnalab.org/teaching/part-iv.-machine-learning/3.machine-learning-with-python.md)
- [1.Precision Medicine - exSEEK](https://book.ncrnalab.org/teaching/part-v.-assignments/1.quiz_exrna.md)
- [Help](https://book.ncrnalab.org/teaching/part-v.-assignments/1.quiz_exrna/help.md)
- [Archive: Version 2018](https://book.ncrnalab.org/teaching/part-v.-assignments/1.quiz_exrna/2018-readme.md)
- [1.1.Data Introduction](https://book.ncrnalab.org/teaching/part-v.-assignments/1.quiz_exrna/2018-readme/2018-1.1-data-introduction.md)
- [1.2.Requirement](https://book.ncrnalab.org/teaching/part-v.-assignments/1.quiz_exrna/2018-readme/2018-1.2-requirement.md)
- [1.3.Helps](https://book.ncrnalab.org/teaching/part-v.-assignments/1.quiz_exrna/2018-readme/2018-1.3-helps.md)
- [2.RNA Regulation - RiboShape](https://book.ncrnalab.org/teaching/part-v.-assignments/2.quiz_rna-regulation.md)
- [2.0.Programming Tools](https://book.ncrnalab.org/teaching/part-v.-assignments/2.quiz_rna-regulation/0.tools.md)
- [2.1.RNA-seq Analysis](https://book.ncrnalab.org/teaching/part-v.-assignments/2.quiz_rna-regulation/1.rna-seq.md)
- [2.2.Ribo-seq Analysis](https://book.ncrnalab.org/teaching/part-v.-assignments/2.quiz_rna-regulation/2.ribo-seq.md)
- [2.3.SHAPE Data Analysis](https://book.ncrnalab.org/teaching/part-v.-assignments/2.quiz_rna-regulation/3.shape.md)
- [2.4.Integration](https://book.ncrnalab.org/teaching/part-v.-assignments/2.quiz_rna-regulation/4.integration.md)
- [3.RNA Regulation - dsRNA Code](https://book.ncrnalab.org/teaching/part-v.-assignments/3.rna-regulation-dsrna.md)
- [4.Single Cell Data Analysis](https://book.ncrnalab.org/teaching/part-v.-assignments/3.single-cell-data-analysis-for-sle.md)
- [Help](https://book.ncrnalab.org/teaching/part-v.-assignments/3.single-cell-data-analysis-for-sle/help.md)
- [5.Model Programming](https://book.ncrnalab.org/teaching/5.model-programming.md)
- [6.AI Agent for Biomedicine](https://book.ncrnalab.org/teaching/6.ai-agent-for-biomedicine.md)
- [Appendix I. Keep Learning](https://book.ncrnalab.org/teaching/appendix/appendix1.keep-learning.md)
- [Appendix II. Databases & Servers](https://book.ncrnalab.org/teaching/appendix/appendix2.databases-servers.md)
- [Appendix III. How to Backup](https://book.ncrnalab.org/teaching/appendix/appendix-iii.-how-to-backup.md)
- [Appendix IV. Teaching Materials](https://book.ncrnalab.org/teaching/appendix/appendix-iv.-teaching.md)
- [Appendix V. Software and Tools](https://book.ncrnalab.org/teaching/appendix/appendix-v.-software-and-tools.md)
- [Appendix VI. Genome Annotations](https://book.ncrnalab.org/teaching/appendix/appendix-vi-genome-and-annotation.md)