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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

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A tool that allows to get UMI counts from a single cell protein assay

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[![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/)