Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods.

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Here, we introduce Hybkit, a Python3 API, and command-line toolkit for analysis of hybrid sequence data in the \"hyb\" file format to enable customizable evaluation and annotation of hybrid characteristics. The Hybkit API includes a suite of python objects for developing custom analyses of hybrid data as well as miRNA-specific analysis methods, built-in plotting of analysis results, and incorporation of predicted miRNA/target interactions in Vienna format.\nAVAILABILITY AND IMPLEMENTATION: Hybkit is provided free and open source under the GNU GPL license at github.com/RenneLab/hybkit and archived on Zenodo (doi.org/10.5281/zenodo.7834299). Hybkit distributions are also provided via PyPI (pypi.org/project/hybkit), Conda (bioconda.github.io/recipes/hybkit/README.html), and Docker (quay.io/repository/biocontainers/hybkit).", "claims": [{"id": "claim-data-access", "statement": "The dataset used for example analyses (Gay et al. 2018a) is available via NCBI Gene Expression Omnibus accession GSE101978: identifiers.org/geo:GSE101978.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38006335", "locator": "sections[13] \"Data availability\" paragraph 2", "quote": "The dataset used for example analyses (Gay et al. 2018a) is available via NCBI Gene Expression Omnibus accession GSE101978: identifiers.org/geo:GSE101978."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38006335"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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