phenomic-ai 0.1.10

A CLI package which facilitates computational biologists with a single cell RNA embedding tool

phenomic-ai

A CLI package which facilitates computational biologists with a single cell RNA embedding tool

Installation

$ pip install phenomic-ai

Usage

pai embed --tmp-dir [tmp_dir_path] --h5ad-path [path to h5ad file] --tissue-organ [tissue organ]

python3 -m pai embed --tmp-dir [tmp_dir_path] --h5ad-path [path to h5ad file] --tissue-organ [tissue organ]

Commands:

• pai main command
• embed sub-command invoking the embedding tool

Parameters:

• --tmp-dir (temporary direcetory) parameter is the root output directory where the downloaded zip files (zips/) and unzipped directories (results/) will be output
• --h5ad-path (h5ad path) parameter is the path to the single cell RNA .h5ad file intended to be uploaded and embeded
• --tissue-organ (tissue/organ) parameter specifies the tissue/organ associated wrt. the single cells
• --output-dir (output directory) directory path to which the results.csv and plotly umap .html files are output
• --model (model) private, authorized users only, requires api key
• --umap-excldue (umap exclude) flag which determines whether to exclude the umap .html files

Examples

pai embed --tmp-dir /tmp/pai/embed --h5ad-path ./anndata.h5ad --tissue-organ adipose

python3 -m pai embed --tmp-dir /tmp/pai/embed --h5ad-path ./anndata.h5ad --tissue-organ adipose

Help

pai embed --help

python3 -m pai embed --help

Support

Email: [e-mail]