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Analysis of SCLC Cell Lines elucidates the landscape of phenotypic heterogeneity enabling diverse SCLC subtypes.

Home Page: https://www.biorxiv.org/content/10.1101/2021.10.27.465593v1

R 22.84% Jupyter Notebook 77.16%
rna-seq-analysis phenotypic-plasticity systems-biology emt cancer-research

sclc-project-code's Introduction

Small Cell Lung Cancer (SCLC)

Computational analysis reveals similarities and differences between SCLC subtypes

Datasets CCLE, GSE73160, GSE7097, GSE10841, GSE45120, GSE62609, GSE66294 & GSE144457 need to be downloaded into the "Datasets" folder. In case of multiple probes, for microarray data, median expression was considered.

ssGSEA scores were generated using the ssgsea-gui.R script available here

Note: Use Transcripts Per Million (TPM) noramalized RNA-seq dataset for ssGSEA

Programming languages used in this analysis

R version 4.0.4 

Bioconductor version 3.11

Python version 3.8.3

Contact

For questions regarding the code deposited in this repository, please reach out to Abhay Singh via email at: ssabhay6 [at] gmail [dot] com

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