CellMiner Cross-Database (CellMinerCDB) & TumorMiner Cancer Pharmacogenomics
Published April 16, 2026 | Version v2
Dataset Open

SclcTumorMinerCDB paper and web files

Authors/Creators

  • 1. ROR icon National Cancer Institute

Description

SclcTumorMinerCDB is a new public web tool for mining Small Cell Lung Cancer (SCLC) patient clinical and genomics data. It is available at https://discover.nci.nih.gov/SclcTumorMinerCDB/

This repository (SclcTumorMinerCDB files) include supplementary files and scripts for the manuscript as well data content needed to run locally the website 

Table of contents

The files needed to run locally the website are:

  • srcContent.rds:  SCLC patient data
  • srcContent_cell.rds: SCLC Broad (CCLE) cell line data

Other files for NMF analysis:

  • NMF_code.zip: Contains two R scripts along with the input gene expression data and sample annotation files located in the input_dataset folder. The scripts must be executed from the same directory that contains the input_dataset folder. The zip file include

    • input_dataset/SCLC_TumoMiner_Sample_annotation.txt: Annotation file for 235 SCLC samples.

    • input_dataset/sclc_Patient_data_xsq_noBER.txt: normalized RNA-seq data in log2(FPKM + 1) format, without batch correction, for the 235 samples.

    • code_untreated.R: R script for NMF clustering and heatmap of clusters in untreated patient samples
    • code_relapse.R: R script for NMF clustering and heatmap of clusters in relapse patient samples

The scripts can be run using the following commands:

    • Rscript code_untreated.R

    • Rscript code_relapse.R

Files

NMF_code.zip

Files (922.2 MB)

Name Size Download all
md5:c333e393d00b10dcdb78e493bf5d8409
28.8 MB Preview Download
md5:a228fdaed9737bcd36d52c1f294ee3d3
241.3 MB Download
md5:08902b51454a8df3e6e71b435cd2d621
652.1 MB Download

Additional details

Software

Repository URL
https://github.com/CBIIT/SclcTumorMinerCDB
Programming language
R