finalized package structure

Reorganized code around three core functions: running the hierarchical model, simulating an experiment, and processing raw experimental data. Standardized command line interface, yaml inputs, and model naming conventions. Lots of bug fixes throughout.

improved hierarchical model

This release includes updates to the posterior sampling and summarization code. It also switches to a more consistent run interface, switching from number of iterations to number of epochs for SVI and MAP inference.

treats multiple plasmid transformations

• Added correction to inferred theta values accounting for the fact cells can pick up more than one plasmid
• Refactored the util submodule from flat to hierarchical
• Tweaks to increase speed of inference
• Updated command line interface to analyze_theta to interface with the model changes
• Lots of docstring clean up
• Added a bunch of unit tests
• Various bug fixes

hierarchical modeling

• Hierarchical modeling analysis now complete.
• Cleaned up analysis and demo notebooks.

v0.2.0: Merge pull request #4 from harmsm/main

Code now does:

• Simulation of experiments
• Processing raw reads (fastq through ln_cfu/condition)
• Independent modeling (extract that for each genotype independently)
• Hierarchical modeling (Bayesian analysis of theta together)
• Epistasis analysis
• Epistasis vs. [titrant] categorization analysis
• Various helpful plotting utilities.

Additionally, the API is now (roughly) stable. I antiquate no major changes to the simulation, raw-processing, or independent modeling code base. I expect to build out the hierarchical modeling codebase and clean up the utilities functions. None of these will be architectural changes, however, just minor refactors.

initial release

This is a first draft of the code that allows simulation and analysis of a transcription factor high-throughput screen. Expect large changes to the API.