scAnnot

Name	scAnnot JSON
Version	0.0.5 JSON
	download
home_page	https://github.com/changebio/scAnnot
Summary	single cell annotation
upload_time	2023-07-06 02:17:29
maintainer
docs_url	None
author	Yin Huang
requires_python	>=3.7
license	Apache Software License 2.0
keywords	nbdev jupyter notebook python
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            scAnnot
================

<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->

This file will become your README and also the index of your
documentation.

## Install

``` sh
pip install scAnnot
```

## How to use

### In command line

#### 1. output the table of predicted lables in csv format

    scAnnot /home/huang_ziliang/project/brain/data/public/human_brain_glial_Fu_2021_PCR/h5/umap.h5ad --output test.csv

#### 2. output the anndata with predicted lables in h5ad

    scAnnot /home/huang_ziliang/project/brain/data/public/human_brain_glial_Fu_2021_PCR/h5/umap.h5ad --output test.h5ad

### In jupyter notebook

    ad=scAnnot('/home/huang_ziliang/project/brain/data/public/human_brain_glial_Fu_2021_PCR/h5/umap.h5ad')

    #show umap from the latent space
    ad=scAnnot('/home/huang_ziliang/project/brain/data/public/human_brain_glial_Fu_2021_PCR/h5/umap.h5ad',show=True)



            

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