# 3dgenome

## 3dgenome

- [Initial page](https://zhonglab.gitbook.io/3dgenome/master.md)
- [Cover](https://zhonglab.gitbook.io/3dgenome/cover.md)
- [Preface](https://zhonglab.gitbook.io/3dgenome/preface.md)
- [Figurelist](https://zhonglab.gitbook.io/3dgenome/figurelist.md)
- [Chap0 Preparation](https://zhonglab.gitbook.io/3dgenome/chap0-preparation.md)
- [0.1 Molecular biology](https://zhonglab.gitbook.io/3dgenome/chap0-preparation/0.1-molecular-biology.md)
- [0.2 Sequencing technologies](https://zhonglab.gitbook.io/3dgenome/chap0-preparation/0.2-sequencing-technologies.md)
- [0.3 RNA-seq Data Mapping & Gene Quantification](https://zhonglab.gitbook.io/3dgenome/chap0-preparation/0.3-rna-seq-data-mapping-and-gene-quantification.md)
- [0.4 RNA-seq Differential Analysis](https://zhonglab.gitbook.io/3dgenome/chap0-preparation/03-rna-seq-differential-analysis.md): Assess different expression levels of genes between our samples at different timepoints, conditions, etc.
- [Chap1 Why we care about 3D genome](https://zhonglab.gitbook.io/3dgenome/chapter1-why-we-care-about-3d-genome.md)
- [1.1 From 2D to 3D nuclear structure](https://zhonglab.gitbook.io/3dgenome/chapter1-why-we-care-about-3d-genome/3d-nuclear-structure.md)
- [1.2 From static to dynamic](https://zhonglab.gitbook.io/3dgenome/chapter1-why-we-care-about-3d-genome/from-static-to-dynamic.md)
- [1.3 From intra to inter chromosomes "talk"](https://zhonglab.gitbook.io/3dgenome/chapter1-why-we-care-about-3d-genome/1.3-from-intra-to-inter-chromosomes-talk.md)
- [1.4 From aggregation to division - phase separation](https://zhonglab.gitbook.io/3dgenome/chapter1-why-we-care-about-3d-genome/1.4-from-aggregation-to-division-phase-separation.md)
- [Chap2 experiment tools for exploring genome interaction](https://zhonglab.gitbook.io/3dgenome/chap2-experiment-tools-for-exploring-genome-interaction.md)
- [2.1 Image based](https://zhonglab.gitbook.io/3dgenome/chap2-experiment-tools-for-exploring-genome-interaction/2.1-image-based.md)
- [2.2 Primary order](https://zhonglab.gitbook.io/3dgenome/chap2-experiment-tools-for-exploring-genome-interaction/2.2-primary-order.md)
- [2.3 Higher order C-techs](https://zhonglab.gitbook.io/3dgenome/chap2-experiment-tools-for-exploring-genome-interaction/2.3-higher-order-c-techs.md)
- [Chap3 Computational analysis](https://zhonglab.gitbook.io/3dgenome/chapter2-computational-analysis.md)
- [3.1 Primary order analysis](https://zhonglab.gitbook.io/3dgenome/chapter2-computational-analysis/3.1-primary-order-analysis.md)
- [3.2 Higer order data analysis](https://zhonglab.gitbook.io/3dgenome/chapter2-computational-analysis/3.2-higer-order-data-analysis.md)
- [3.2.1 Read mapping consideration](https://zhonglab.gitbook.io/3dgenome/chapter2-computational-analysis/3.2-higer-order-data-analysis/read-mapping-consideration.md)
- [3.2.2 Analytical Pipelines](https://zhonglab.gitbook.io/3dgenome/chapter2-computational-analysis/3.2-higer-order-data-analysis/analytical-pipelines.md)
- [GITAR Pipeline](https://zhonglab.gitbook.io/3dgenome/chapter2-computational-analysis/3.2-higer-order-data-analysis/analytical-pipelines/gitar-pipeline.md): GITAR website: https://www.genomegitar.org
- [HiC-Pro Pipeline](https://zhonglab.gitbook.io/3dgenome/chapter2-computational-analysis/3.2-higer-order-data-analysis/analytical-pipelines/hic-pro-pipeline.md)
- [3.2.3 TAD calling algorithms](https://zhonglab.gitbook.io/3dgenome/chapter2-computational-analysis/3.2-higer-order-data-analysis/tad-calling-algorithms.md)
- [3.3 3D structure](https://zhonglab.gitbook.io/3dgenome/chapter2-computational-analysis/3.3-3d-structure.md)
- [Chap4 RNA-genome interaction](https://zhonglab.gitbook.io/3dgenome/chap4-rna-genome-interaction.md)
- [4.1 Experimental Methods](https://zhonglab.gitbook.io/3dgenome/chap4-rna-genome-interaction/4.1-experimental-methods.md)
- [4.2 Computational Analysis](https://zhonglab.gitbook.io/3dgenome/chap4-rna-genome-interaction/4.2-computational-analysis.md)
- [Chap5 Integrative Data Visualization Tools](https://zhonglab.gitbook.io/3dgenome/chap4-integrative-data-visualization-tools.md)
- [5.1 GIVE](https://zhonglab.gitbook.io/3dgenome/chap4-integrative-data-visualization-tools/4.1give.md)
- [5.2 HiGlass](https://zhonglab.gitbook.io/3dgenome/chap4-integrative-data-visualization-tools/4.2-higlass.md)
- [Chap6 4DN Project](https://zhonglab.gitbook.io/3dgenome/chap5-4dn-project.md)
- [Appendix](https://zhonglab.gitbook.io/3dgenome/appendix-homework.md)
- [Homework](https://zhonglab.gitbook.io/3dgenome/appendix-homework/homework.md)
- [Student's presentation](https://zhonglab.gitbook.io/3dgenome/appendix-homework/students-note.md)
- [A Brief Introduction to Machine Learning](https://zhonglab.gitbook.io/3dgenome/appendix-homework/students-note/a-brief-introduction-to-machine-learning.md): Contributed by Victoria Tom, BENG183 2018 Fall. UCSD
- [Precision medicine](https://zhonglab.gitbook.io/3dgenome/appendix-homework/students-note/precision-medicine.md): Contributed by Reysha Patel, BENG183 2018 Fall. UCSD
- [CHIP-Seq](https://zhonglab.gitbook.io/3dgenome/appendix-homework/students-note/chip-seq.md): Contributed by Yiyang Yin, BENG183 2018 Fall. UCSD