Chapter 8 References

8.1 Python

https://www.runoob.com/python/python-basic-syntax.html

8.2 Analysis of single cell RNA-seq data 分析流程

https://scrnaseq-course.cog.sanger.ac.uk/website/index.html

Orchestrating Single-Cell Analysis with Bioconductor # 分析流程 http://bioconductor.org/books/release/OSCA/

https://github.com/singleron-RD/CeleScope

https://scrnaseq-course.cog.sanger.ac.uk/website/index.html

https://satijalab.org/seurat/

TO do https://github.com/bvieth/scRNA-seq-pipelines

8.3 Assigning cell types with SingleR # 细胞类型注释

http://bioconductor.org/books/release/SingleRBook/

8.4 Museum of Spatial Transcriptomics # 空转简史

https://bookdown.org/lambdamoses/museumst/

8.5 ATAC 分析 Archr

https://www.archrproject.com/bookdown/index.html#section

8.6 monocl and velocyto

http://cole-trapnell-lab.github.io/monocle-release/docs/

http://velocyto.org/velocyto.py/index.html

https://www.jianshu.com/p/d2991fa79a3e

https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html

8.7 integraton

https://satijalab.org/seurat/articles/integration_large_datasets.html

8.8 Gene set enrichment

http://yulab-smu.top/clusterProfiler-book/

https://www.bioconductor.org/packages/release/bioc/html/GSVA.html

http://bioconductor.org/packages/3.12/data/annotation/

如何取子集 https://www.jianshu.com/p/50e2b6ff10d8

提取Seurat数据做GSEA https://www.jianshu.com/p/e9b59353cd3a

http://www.bioconductor.org/packages/release/bioc/vignettes/fgsea/inst/doc/fgsea-tutorial.html

8.9 转录因子

http://bioinfo.life.hust.edu.cn/AnimalTFDB#!/download

8.10 Reproducible research

Tambalo M, Mitter R, Wilkinson DG. A single cell transcriptome atlas of the developing zebrafish hindbrain. Development. 2020 Mar 16;147(6):dev184143. doi: 10.1242/dev.184143. PMID: 32094115; PMCID: PMC7097387.

https://github.com/crickbabs/ZebrafishDevelopingHindbrainAtlas

8.11 基因调控

GENIE3 || 基因调控网络推断 https://www.jianshu.com/p/893654f39a78

RcisTarget || 从基因列表到调控网络 https://www.jianshu.com/p/6e1d71db4220

8.12 cell annotation

http://biocc.hrbmu.edu.cn/CellMarker/

https://panglaodb.se/

https://www.jianshu.com/p/01a594013e8a #clusterProfiler也能做细胞类型鉴定

8.13 空间分析

https://www.jianshu.com/nb/48767585

http://www.cellchat.org/ https://github.com/sqjin/CellChat