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scanscn

A tool to identify small cell neuroendocrine (SCN) features from transcriptomic data.

https://github.com/fesedebe/scanscn

Science Score: 44.0%

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Repository

A tool to identify small cell neuroendocrine (SCN) features from transcriptomic data.

Basic Info
  • Host: GitHub
  • Owner: fesedebe
  • License: mit
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 17.6 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created 11 months ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

ScanSCN

ScanSCN is a toolkit for identifing and analyzing small cell neuroendocrine (SCN) molecular features in transcriptomics datasets.

Overview

It supports R, Python and Snakemake workflows for both bulk and single-cell RNA-seq data and is applicable across a range of cancer types.

Features

Bulk RNA-seq

  • Signature Enrichment: Enrichment against curated resistance gene sets
  • SCN Scoring: PCA projection of query expression onto SCN reference
  • Similarity Assessment: Compare DEGs, expression, and pathway trends vs known SCN profiles

Single-cell RNA-seq

  • Preprocessing: Mitochondrial filtering, doublet detection (scDblFinder), ambient RNA correction (DecontX)
  • Normalization & Integration: SCTransform with optional cell cycle regression, RPCA or Harmony integration
  • Clustering & DE: Leiden clustering, MAST-based marker identification
  • Trajectory Analysis: Monocle 3 pseudotime inference
  • Signature Scoring: AddModuleScore for SCN and other resistance signatures
  • SCN Gene Prioritization: Cell classification → pseudobulk aggregation → DE feature selection → Ensemble ML model training for feature importance ranking

Owner

  • Login: fesedebe
  • Kind: user

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: ScanSCN
message: 'If you use this software, please cite it as below.'
type: software
authors:
  - given-names: Favour
    family-names: Esedebe
    orcid: 'https://orcid.org/0000-0001-6167-0647'
repository-code: 'https://github.com/fesedebe/ScanSCN'
license: MIT

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