目录

Bioinformatic

Database

Title Site Note
GEO https://www.ncbi.nlm.nih.gov/geo/
Genbank https://www.ncbi.nlm.nih.gov/genbank/
DDBJ https://www.ddbj.nig.ac.jp/index-e.html
CNGBdb https://db.cngb.org/
EMBL https://www.ebi.ac.uk/ena/browser/home
ArrayExpress https://www.ebi.ac.uk/arrayexpress/
CCLE https://portals.broadinstitute.org/ccle
ARCHS4 https://maayanlab.cloud/archs4/index.html
GDC-TCGA https://portal.gdc.cancer.gov/ 肿瘤
GDAC http://gdac.broadinstitute.org/ TCGA整合库
cBioPortal http://www.cbioportal.org/ 肿瘤
UCSC https://genome.ucsc.edu/
miRbase http://www.mirbase.org/ miRNA
UCSC Xena https://xenabrowser.net/datapages/ 在线分析
GEPIA http://gepia.cancer-pku.cn/ 可视化
http://firebrowse.org/ 可视化
http://www.oncolnc.org/ 可视化
Ensenbl https://www.ensembl.org/index.html
KEGG https://www.genome.jp/kegg/ 通路
Starbase http://starbase.sysu.edu.cn/
https://zhuanlan.zhihu.com/p/79626339 生物信息学数据库及在线工具
GeneCards https://www.genecards.org/
Gene wiki https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Molecular_Biology/Genetics/Gene_Wiki

一些参考

GSEA https://gseapy.readthedocs.io/en/latest/gseapy_example.html
LOG2FC Video https://www.youtube.com/watch?v=HH3Mll4W5WE
Visualization of functional enrichment result https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html
Processing raw 10X Genomics single-cell RNA-seq data https://swaruplab.bio.uci.edu/tutorial/cellranger/cellranger-rna.html

处理步骤

RNA-seq https://zhuanlan.zhihu.com/p/37196518

可视化

  1. Venn 文氏图
  2. 生存曲线
  3. 箱式图
  4. 热图
  5. 相关矩阵

一些实验室

THE ABDUS-SABOOR LAB https://www.abdus-saboorlab.com/
GAO Lab https://chengaolab.com/