pymportx 0.2.0

Pymportx is a Python package designed for fast gene count estimation using transcript quantification files generated by pseudoalignment or quasi-mapping tools. It is a Python adaptation of the widely-used Tximport R package from Bioconductor.

pymportx

pymportx is a Python package designed for fast gene count estimation using transcript quantification files generated by pseudoalignment or quasi-mapping tools. It is a Python adaptation of the widely-used tximport R package from Bioconductor.

Documentation

Documentation is made available at https://pymportx.readthedocs.io.

Example

from pymportx import salmon

results = salmon.read_salmon(salmon_folder_paths,
                             tx_out=False,
                             tx2gene=tx2gene_file_path,
                             countsFromAbundance='no')

Citation

If you use pymportx in your research, please cite the following paper:

Pena Gonzalez, P., Lozano-Paredes, D., Rojo, J. L., Bote-Curiel, L., & Sanchez-Arevalo Lobo, V. J. (2024). Pymportx: Facilitating Next-Generation Transcriptomics Analysis in Python. bioRxiv. doi:10.1101/2024.07.12.598873

License

This project is licensed under the MIT License. See the LICENSE file for more details.

Contact

For more information, you can contact us through [e-mail] or [e-mail].