https://github.com/Hoohm/CITE-seq-Count

A tool that allows to get UMI counts from a single cell protein assay
https://github.com/Hoohm/CITE-seq-Count

10x citeseq dropseq single-cell

Last synced: 9 months ago
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A tool that allows to get UMI counts from a single cell protein assay

• Host: GitHub
• URL: https://github.com/Hoohm/CITE-seq-Count
• Owner: Hoohm
• License: mit
• Created: 2017-08-07T20:32:40.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2024-07-22T22:56:44.000Z (over 1 year ago)
• Last Synced: 2025-03-08T10:47:56.485Z (10 months ago)
• Topics: 10x, citeseq, dropseq, single-cell
• Language: Python
• Homepage: https://hoohm.github.io/CITE-seq-Count/
• Size: 787 KB
• Stars: 81
• Watchers: 10
• Forks: 44
• Open Issues: 45
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE.txt

Awesome Lists containing this project

• awesome-single-cell - CITE-seq-Count - [python] Cite-seq-Count is a python package that deals with Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and cell hashing data. [CITE-seq](https://cite-seq.com/) is a multimodal single cell phenotyping method that allows for immunophenotyping of cells with a potentially limitless number of markers and unbiased transcriptome analysis using existing single-cell sequencing approaches. (Software packages / Multi-assay data integration)

README

          
[![DOI](https://zenodo.org/badge/99617772.svg)](https://zenodo.org/badge/latestdoi/99617772)

# CITE-seq-Count

A python package that allows to count antibody TAGS from a [CITE-seq](https://www.nature.com/articles/nmeth.4380) and/or [cell hashing](https://www.biorxiv.org/content/early/2017/12/21/237693) experiment.

IMPORTANT NEWS

------------------------------------------

There was a major bug in version 1.3.4 of CITE-seq-Count. The results were in read counts and not in UMI counts.

This is fixed in version 1.4.0 or above. Please rerun your data as this might provide a cleaner result for your data.

Here is the website referencing the wetlab protocols needed https://cite-seq.com/

Installation

-------------------------------------------

```

pip install CITE-seq-Count==1.4.5

```

The official documentation can be found [here](https://hoohm.github.io/CITE-seq-Count/)