Changelog

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Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]#

Added#

  • mantispy.io: read_profiles for profile files, CellProfiler ExportToSpreadsheet directories and CytoTable parquet parts; read_plate for a Cell Painting Gallery source or an ExportForSpatialData plate folder as SpatialData; read_jump, read, write and validate

  • mantispy.ds: the generated synthetic_plate and blobs; bbbc021, rohban, pki and jump_target2 with the annotations the analyses need; nine further Cell Painting Gallery accessions

  • mantispy.ds: jump_cells, jump_export and jump_plate, the single cells, one CellProfiler export directory and the images of BR00121438, the plate jump_target2 reads well profiles for; jump_cells(selected=True) returns only the features var['selected'] marks

  • mantispy.pp: quality control at cell, image and well level, normalization, feature selection, outlier detection, sphering, plate-position correction and Harmony

  • mantispy.tl: aggregation, consensus profiles, mAP and replicate retrieval, hit calling, effect sizes, dose response, mechanism-of-action retrieval and enrichment, differential features, transport across sites and single-cell heterogeneity

  • mantispy.metrics, mantispy.get and mantispy.pl, for judging a correction, reading results out and plotting them

  • mantispy.settings, holding the verbosity and the cache directory the datasets download into

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