Citations / references for pandas usage in the bio-medical sciences

[jorisvandenbossche]

Gathering some refs of packages / projects that use pandas (partly based on sklearn's proposal):

• QIIME microbiome bioinformatics platform (https://qiime2.org/, https://github.com/qiime2/qiime2). Citation: https://doi.org/10.1038/s41587-019-0209-9
• BioPandas: working with molecular structures in pandas DataFrames(https://rasbt.github.io/biopandas/, https://github.com/rasbt/biopandas). Citation: http://joss.theoj.org/papers/10.21105/joss.00279
• Starfish: https://github.com/spacetx/starfish (but not sure how fundamental their use of pandas is; it seems a project related to CZI)
• mne-python (optional dependency). https://doi.org/10.5281/zenodo.3133134
• scikit-allel: https://github.com/cggh/scikit-allel (optional dependency). https://doi.org/10.5281/zenodo.3238280
• MSMBuilder: https://github.com/msmbuilder/msmbuilder.
• nistats: Modeling and statistical inference on fMRI data in Python (https://github.com/nistats/nistats).

Searching for citations of the McKinney (https://scholar.google.com/scholar?start=0&q=biomedical&hl=en&as_sdt=1000005&sciodt=0,16&cites=4302385174768819463&scipsc=1). Some potentially interesting items:

• https://peerj.com/preprints/27352.pdf: Bioinformatics software for genomic: a systematic review on GitHub -> mentions Python in general as the most used programming language in bioinformatics