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Core functions for pycisTarget and the SCENIC tool suite

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Core functions for pycisTarget and the SCENIC tool suite

ctxcore is part of the SCENIC Suite of tools! See the main SCENIC website for additional information and a full list of tools available.


ctxcore is available on PyPI and can be installed with pip.

$ pip install ctxcore

After installing ctxcore you can use it like any other Python module.

Here is a simple example:

import ctxcore
# Fill this section in with the common use-case.

The API Reference provides API-level documentation.

Change Log

Version History

  • Remove unused RankingsDatabase classes and conversion functions.

  • Add CisTargetDatabase class for reading rankings/scores for regions/genes from a cisTarget scores or rankings database (only Feather v2 format), which requires pyarrow >= 8.0.0 instead of <=0.17.1 needed for the old FeatherRankingDatabase class.

  • Update FeatherRankingDatabase to use CisTargetDatabase to read cisTarget databases.

  • Reformat code and update type annotations.

  • Add support for reading rankings databases created by create_cisTarget_databases as the index column in the Feather file is “motifs” or “tracks” instead of “features”.

  • Project created.

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