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Refactor the dynamics#549

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Sichao25 wants to merge 36 commits intoaristoteleo:masteraristoteleo/dynamo-release:masterfrom Sichao25:refactorSichao25/dynamo-release:refactorCopy head branch name to clipboard

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Commits on Jun 2, 2023

• create Dynamics class

  Sichao25

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• func to methods

  Sichao25

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• add sanity check method

  Sichao25

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Commits on Jun 7, 2023

• optimize structure

  Sichao25

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Commits on Jun 12, 2023

• reconstruct basic framework

  Sichao25

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• implement caller

  Sichao25

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Commits on Jun 13, 2023

• add sskin class

  Sichao25

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• modify the structure of labeled dynamics

  Sichao25

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• implement existing mix methods

  Sichao25

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• finalize wrapper

  Sichao25

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• debug wrapper and kin

  Sichao25

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Commits on Jun 14, 2023

• add base docstr and all typing

  Sichao25

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• add docstr for subclass

  Sichao25

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Commits on Jun 16, 2023

• add to tl init

  Sichao25

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• debug

  Sichao25

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Commits on Jun 19, 2023

• add subclass KineticsStormDynamics and upload storm.py to support Storm's three stochastic model

  QiangweiPeng

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• Modify the relevant code to support cell-specific beta

  QiangweiPeng

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• Add code to moments.py that calculates the moments needed for the storm method.

  QiangweiPeng

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Commits on Jun 21, 2023

• Added the parameter inference method storm for one-shot experiments

  QiangweiPeng

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• rename functions

  Sichao25

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Commits on Jul 6, 2023

• Merge branch 'Sichao25:master' into add_storm

  QiangweiPeng

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• Delete scEU-seq_CellCycle_CSP_CSZIP.py

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  QiangweiPeng

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• Delete cell_cycle_CSPss.py

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  QiangweiPeng

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Commits on Jul 7, 2023

• Merge branch 'add_storm' into refactor

  QiangweiPeng

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• reformat tab space

  Sichao25

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• rename storm func

  Sichao25

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• reformat storm

  Sichao25

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Commits on Jul 25, 2023

• create kinetic params est func

  Sichao25

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Commits on Jul 26, 2023

• create ss fit functions

  Sichao25

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• create kinetic params estimation class

  Sichao25

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• call refactored params estimation

  Sichao25

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Commits on Jul 27, 2023

• create docstr

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Commits on Aug 22, 2023

• delete tutorial script

  Sichao25

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Commits on Sep 29, 2023

• Merge branch 'master' into refactor

  Sichao25

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• Merge branch 'master' into refactor

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Commits on Oct 10, 2023

• Merge branch 'master' into refactor

  Sichao25

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