https://github.com/broadinstitute/infercnv

Inferring CNV from Single-Cell RNA-Seq
https://github.com/broadinstitute/infercnv

Last synced: 4 months ago
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Inferring CNV from Single-Cell RNA-Seq

• Host: GitHub
• URL: https://github.com/broadinstitute/infercnv
• Owner: broadinstitute
• License: other
• Created: 2016-03-14T21:53:54.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2025-02-01T21:53:41.000Z (over 1 year ago)
• Last Synced: 2025-05-03T07:18:52.024Z (about 1 year ago)
• Language: R
• Homepage:
• Size: 22.6 MB
• Stars: 607
• Watchers: 38
• Forks: 170
• Open Issues: 225
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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• top-life-sciences - **broadinstitute/infercnv** - Cell RNA-Seq<br><img src='https://github.com/HubTou/topgh/blob/main/icons/gstars.png'> 520 <img src='https://github.com/HubTou/topgh/blob/main/icons/forks.png'> 159 <img src='https://github.com/HubTou/topgh/blob/main/icons/watchers.png'> 42 <img src='https://github.com/HubTou/topgh/blob/main/icons/code.png'> R <img src='https://github.com/HubTou/topgh/blob/main/icons/license.png'> specific <img src='https://github.com/HubTou/topgh/blob/main/icons/last.png'> 2020-02-07 20:29:28 | (Ranked by starred repositories)

README

          

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>InferCNV is no longer supported. Please explore alternatives such as InferCNA (https://jlaffy.github.io/infercna/)[https://jlaffy.github.io/infercna/], CopyKAT (https://github.com/navinlabcode/copykat)[https://github.com/navinlabcode/copykat], and Numbat (https://github.com/kharchenkolab/numbat)[https://github.com/kharchenkolab/numbat]

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# Subclustering

Subclustering resolution is one of the primary settings that will need to be adjusted in most runs to avoid oversplitting. The tutorial below explains how it works and details about it can also be found on the [wiki](https://github.com/broadinstitute/infercnv/wiki/infercnv-tumor-subclusters#tumor-subclustering-by-leiden-clustering-preferred).

# Documentation

### Full documentation

Visit project [wiki](https://github.com/broadinstitute/inferCNV/wiki) for InferCNV documentation.

### Infercnv video tutorial

A **video** tutorial giving on overview of infercnv features and how to run an analysis can be found below **(click on the image)**:

[![Tutorial: Running infercnv](http://img.youtube.com/vi/-qOcHAavZT8/0.jpg)](http://www.youtube.com/watch?v=-qOcHAavZT8 "Tutorial: Running infercnv")