Efficient querying of genomic databases for single-cell RNA-seq with gget [article]

Laura Luebbert, Lior Pachter
2022 bioRxiv   pre-print
AbstractMotivationA recurring challenge in interpreting single-cell RNA-seq data is the assessment of results in the context of existing genomic databases. Currently, there is no tool implementing automated, easy programmatic access to information stored in a diverse collection of large, public genomic databases.Resultsgget is a free and open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but
more » ... le modules, each designed to facilitate one type of database querying required for single-cell RNA-seq data analysis in a single line of code.AvailabilityThe manual and source code are available at https://github.com/pachterlab/gget.Contactlpachter@caltech.edu
doi:10.1101/2022.05.17.492392 fatcat:y2qft3qceza57j5j7q4ybrruyi