WEB-based analysis

TIMER : A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells

> TIMER, https://doi.org/10.1158/0008-5472.CAN-17-0307

> TIMER2.0, https://doi.org/10.1093/nar/gkaa407 

http://timer.cistrome.org/

http://timer.comp-genomics.org/

 

GEPIA : Gene Expression Profiling Interactive Analysis

> GEPIA, https://doi.org/10.1093/nar/gkx247

> GEPIA2, https://doi.org/10.1093/nar/gkz430

> GEPIA2021, https://doi.org/10.1093/nar/gkab418

http://gepia.cancer-pku.cn/

http://gepia2.cancer-pku.cn/

http://gepia2021.cancer-pku.cn/

https://github.com/zwj-tina/GEPIA2021

 

Survival analysis

> https://doi.org/10.1016/j.cell.2018.02.052

https://nborcherding.shinyapps.io/TRGAted/

 

Therapeutic Target Database

> TTD, https://doi.org/10.1093/nar/30.1.412

> Update of TTD, https://doi.org/10.1093/nar/gkp1014

> Therapeutic target database 2020, https://doi.org/10.1093/nar/gkz981

http://db.idrblab.net/ttd/

 

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Data Hubs

https://xenabrowser.net/hub/

https://xenabrowser.net/datapages/?cohort=TCGA Pan-Cancer

https://xenabrowser.net/datapages/?dataset=tcga_RSEM_gene_tpm

https://xenabrowser.net/datapages/?dataset=gtex_RSEM_gene_tpm

 

 

Reference

- https://github.com/mdozmorov/Immuno_notes

- https://github.com/Sun-lab/CARseq_pipelines

- https://rtcga.github.io/RTCGA/reference/index.html

- https://gdc.cancer.gov/about-data/publications/panimmune

- https://github.com/BNadel/GEDIT

- https://github.com/ysuzukilab/Cibersortx