DROMA

Drug Response Omics association MAp (DROMA, 卓玛)

DROMA is a comprehensive database and analysis tool that integrates the largest published studies investigating cancer response to chemical compounds and the associations between drug sensitivity and multi-omics data (mRNA, CNV, protein, mutation, etc.) across various cancer models including PDC (Patient-Derived Cells), PDO (Patient-Derived Organoids), and PDX, human data are under development.

Main components

• Projects about data:

DROMA_DB: mugpeng/DROMA_DB: Sqlite db and DromaSet obj for Drug Response Omics association MAp. (DROMA)

DROMA_Set: mugpeng/DROMA_Set: DROMASet is a comprehensive R package for managing and analyzing drug response and omics data across multiple projects. It provides a robust framework for handling complex multi-omics datasets with integrated drug sensitivity information, enabling seamless cross-project comparisons and analyses.

• Projects about analysis:

DROMA_R: mugpeng/DROMA_R: R package for DROMA.

DROMA_Web: mugpeng/DROMA_Web: Shiny website for Drug Response Omics association MAp. (DROMA)

• AI and AI agent:

DROMA_MCP: [mugpeng/DROMA_MCP: DROMA MCP Server bridges the gap between AI assistants and cancer pharmacogenomics analysis by providing a natural language interface to the DROMA.R and DROMA.Set packages.](https://github.com/mugpeng/DROMA_MCP)

• Under development:

DROMA_MCP, DROMA_AI, DROMA_Augur, DROMA_py

Statistics Info

Include 17 datasets now(11 cell line, 2 PDC, 3 PDO, 1 PDX), totally 2599 unique samples and 56398 unique drugs.

Citation

If you use DROMA or any subprojects(DB, R, web…) in your research, please cite:

Li, S., Peng, Y., Chen, M. et al. Facilitating integrative and personalized oncology omics analysis with UCSCXenaShiny. Commun Biol 7, 1200 (2024). https://doi.org/10.1038/s42003-024-06891-2

Milestone

0526 v0.4 andata

坂本龍一:【氛围感｜andata (Electric Youth Remix)】 https://www.bilibili.com/video/BV1v7kAY7Eoi/?share_source=copy_web&vd_source=bd40fa636d7a7f4f2a51596fed85e2b0

0513 v0.3

Refactor App.R and Modules: Update version to 0.3.

• add new datasets, now have in vivo data now(Xeva PDX dataset), totally include 17 datasets now(11 cell line, 2 PDC, 3 PDO, 1 PDX)

• add new module, and enhance drug feature analysis.
• Remove deprecated Rmd files and adjust data loading paths.
• Update BatchFeature and DrugOmicPair modules for improved functionality and user experience.
• Functionize all functions in modules and put them under Package_Function/ preparing for making DROMA R package.
• fix some bugs.

0319

I will attend UM PhD seminar, welcome!

0318 v0.2

The stable version v0.2 is online now in UM network: http://fscpo.fhs.um.edu.mo/DROMA_DB/ Btw, please be patient, it may take 10-20s when first time start it. :)

This update includes:

1. Add denglab three PDO data(deng1(breast), deng2(colon), deng3(nasopharynx)) with paired RNAseq, IC50 and annotation data;
2. Harmonize cell line drug and cell names also the annotation data;
3. Add choice to filter data for a specific tumor type(Breast, lung…) or data type(cell line, PDO), and a global setting page to set data. Now all continous data is transformed to by z-score in default, which allow to add a merged result for visualization ;
4. Add several figures and some visualization-related improvement.