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 is made available at https://pymportx.readthedocs.io.
from pymportx import salmon
results = salmon.read_salmon(salmon_folder_paths,
tx_out=False,
tx2gene=tx2gene_file_path,
countsFromAbundance='no')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
This project is licensed under the MIT License. See the LICENSE file for more details.
For more information, you can contact us through [email protected] or [email protected].
For additional test datasets, scripts, and results related to the paper, you can access this shared folder.