https://kharchenkolab.github.io/numbat/

Haplotype-aware CNV analysis from single-cell RNA-seq
https://kharchenkolab.github.io/numbat/

cancer-genomics cnv-detection phylogeny single-cell single-cell-analysis single-cell-rna-seq

Last synced: 4 months ago
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Haplotype-aware CNV analysis from single-cell RNA-seq

• Host: GitHub
• URL: https://kharchenkolab.github.io/numbat/
• Owner: kharchenkolab
• License: other
• Created: 2021-05-25T14:49:18.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2024-03-17T23:16:46.000Z (4 months ago)
• Last Synced: 2024-03-17T23:33:09.295Z (4 months ago)
• Topics: cancer-genomics, cnv-detection, phylogeny, single-cell, single-cell-analysis, single-cell-rna-seq
• Language: R
• Homepage: https://kharchenkolab.github.io/numbat/
• Size: 360 MB
• Stars: 139
• Watchers: 9
• Forks: 20
• Open Issues: 58
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• repo-5916-awesome-genome-visualization - numbat - genome-visualization/numbat.png) (Single cell)
• awesome-genome-visualization - numbat

README

        
# Numbat

[![](https://circleci.com/gh/kharchenkolab/numbat.svg?style=svg)](https://app.circleci.com/pipelines/github/kharchenkolab/numbat)

[![CRAN status](https://www.r-pkg.org/badges/version/numbat)](https://cran.r-project.org/package=numbat)

[![CRAN downloads](https://cranlogs.r-pkg.org/badges/numbat)](https://cran.r-project.org/package=numbat)



Numbat is a haplotype-aware CNV caller from single-cell and spatial transcriptomics data. It integrates signals from gene expression, allelic ratio, and population-derived haplotype information to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 

Numbat can be used to:

 1. Detect allele-specific copy number variations from scRNA-seq and spatial transcriptomics

 2. Differentiate tumor versus normal cells in the tumor microenvironment 

 3. Infer the clonal architecture and evolutionary history of profiled tumors. 

![image](https://user-images.githubusercontent.com/13375875/153020818-2e782689-09db-427f-ad98-2c175021a936.png)

Numbat does not require paired DNA or genotype data and operates solely on the donor scRNA-seq data (for example, 10x Cell Ranger output). For details of the method, please checkout our paper:

> [Teng Gao, Ruslan Soldatov, Hirak Sarkar, Adam Kurkiewicz, Evan Biederstedt, Po-Ru Loh, Peter Kharchenko. Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes. Nature Biotechnology (2022).](https://www.nature.com/articles/s41587-022-01468-y)

# User Guide

For a complete guide, please see [Numbat User Guide](https://kharchenkolab.github.io/numbat/).

# Questions?

We appreciate your feedback! Please raise a github [issue](https://github.com/kharchenkolab/numbat/issues) for bugs, questions and new feature requests. For bug reports, please attach full log, error message, input parameters, and ideally a reproducible example (if possible).