search

openbiox / UCSCXenaShiny

📊 An R package for interactively exploring UCSC Xena https://xenabrowser.net/datapages/; Book: https://lishensuo.github.io/UCSCXenaShiny_Book; App online: https://shiny.hiplot.cn/ucsc-xena-shiny/, https://shiny.zhoulab.ac.cn/UCSCXenaShiny
https://openbiox.github.io/UCSCXenaShiny/
GNU General Public License v3.0
83 stars 29 forks source link

Request for R Code for TCGA Association Analysis Features in Xena hiplot #285

Open quiquemedina opened 7 months ago

quiquemedina commented 7 months ago

Dear @ShixiangWang ,

I am following up on my request from two weeks ago regarding the R code for the new features in TCGA Association analysis, specifically those enabling queries of CpG sites and gene coordinates (hg38) within the Xena hiplot platform.

I apologize if my repeated inquiries seem excessive. However, I have been unable to locate the relevant code in the GitHub repository UCSCXenaShiny for use in R.

Could you kindly guide me to the specific location or path where this code can be found?

To illustrate my requirement, I am particularly interested in the process for querying CpG sites associated with the RCAN2 gene in Esophageal Carcinoma (ESCA). The steps I am referring to are as follows:

TCGA Association Analysis S1 Preset: a. Select cancer type: ESCA b. Choose modified dataset: i. TOIL-DNA Methylation ii. 450k iii. Gene: RCAN2 iv. Specify minimum and maximun coordinates to delimit CpG sites:

  1. 46391143
  2. 46472267 c. Include 3 CpG sites S2 Get Data: a. Query data b. Define molecular profile: i. Methylation ii. Identifier: RCAN2 c. Further data query: i. Tumor index ii. Tumor stemness iii. Identifiers: RNAss S3 Analysis & Visualize: a. Perform Correlation analysis (Spearman) Your assistance with this matter would be greatly appreciated. Thank you for your understanding and support.

Best regards,

Enrique

ShixiangWang commented 7 months ago

@quiquemedina Thanks for your good points as always. @lishensuo has given our initial response in the https://github.com/openbiox/UCSCXenaShiny/issues/257#issuecomment-1841865498. We have considered this. However, the server logic and shiny modules have not been split into different parts. We need some time to implement different functions and combine them to serve features directly with R functions. Thanks for your query and patience.