CellTypeGenomics is an open-source Python package designed to analyze the cell-type origins of genes using Human Protein Atlas data. It helps to identify genes that are potentially over-represented or under-represented in specific cell types, providing insights that are crucial for understanding various biological processes and diseases.
- Gene Analysis: Analyzes a list of gene Ensembl IDs and returns a sorted pandas DataFrame, highlighting genes that are potentially over- or under-represented in certain cell types.
- Data Source: Leverages the comprehensive gene expression data available from the Human Protein Atlas.
To install CellTypeGenomics, run the following command in your terminal:
pip install celltypegenomicsHere's how to use the CellTypeGenomics package to analyze your gene list:
from celltypegenomics import celltypefishertest
# Specify an optional alpha for significance (default: 0.05)
result = celltypefishertest(list_of_ensembl_ids, alpha=0.05)
print(result)Replace list_of_ensembl_ids with your list of gene Ensembl IDs.
For more information, updates, or to contribute to the project, please visit our GitHub Repository.
CellTypeGenomics is released under the MIT license. See the LICENSE file for more details.