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Recent Releases of speclet

speclet - v1.0.0

Final release of 'speclet'

While incomplete, this project was a strong proof-of-concept for the development of a complex Bayesian linear model fit to large-scale CRISPR screen data.

Below is a collection of all the PRs for this repo as a way of recognizing the work that went into the research project.

What's Changed

  • Model design experimentation by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/1
  • Update master with subset-data branch by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/5
  • Python type hints by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/6
  • Data subset model by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/11
  • Data subset model (merge to fix sync issues with GitHub) by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/13
  • Experimentation with modeling a subset of the data by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/14
  • CRC model experimentation and workflow proof-of-concept by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/16
  • Tests against modules in analysis by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/19
  • Remove old cruft from attempting to fit a mimic of CERES by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/21
  • CRC model 1 to model-fitting pipeline by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/26
  • Use Papermill to parameterize model report notebooks by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/27
  • Project reorganization by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/29
  • Reorganize pipeline by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/30
  • Design CRC Model 2 by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/31
  • PPC LOO-CV by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/34
  • Fix many logging issues by making a separate module. by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/35
  • PyMC3 models as classes by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/38
  • Update pipeline for object-oriented model fitting by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/39
  • Create the first in a series of CERES mimicking models by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/40
  • Simulation based calibration pipeline by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/41
  • Flake8 code formatting by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/43
  • Optional copy number covariate in CERES model by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/44
  • Add an optional varying intercept for sgRNA | gene to CERES by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/45
  • Update and run pipelines by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/48
  • Add and fit a new model: SpecletOne by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/50
  • Refactor model system by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/51
  • Update pipelines by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/52
  • Add SpecletTwo model by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/53
  • analysis: fit SpecletOne and Two by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/54
  • Optional KRAS covariate in SpecletTwo and reorganize model structure of fitting pipeline by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/55
  • SpecletThree and Four by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/56
  • Separate mcmc chains by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/58
  • Non-centered parameterization of SpecletThree (PoC) by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/62
  • Non-centered parameterization of SpecletFour by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/64
  • Refactor the munging process into a single Snakemake pipeline by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/65
  • Update data with Project SCORE and fix some known issues. by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/66
  • Add SpecletFive and SpecletSix models by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/67
  • Update SBC pipeline by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/68
  • Build SpecletSeven as a deep hierarchical model by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/73
  • Refactor SBC and model-fitting pipelines by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/74
  • Update project documentation by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/77
  • Improved efficiency of CI by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/78
  • SBC refactor by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/79
  • Snakemake pipeline build in nightly project build CI by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/85
  • SBC limited run by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/86
  • Test sprint (increase coverage over some modules) by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/87
  • Model standardization refactor by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/88
  • Configuration-driven system for entire project by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/92
  • Munge pipeline refactor by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/97
  • Fit models by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/99
  • Sp7 parameterizations by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/104
  • SBC uniformity test by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/105
  • SpecletSimple model for easy experimentation by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/106
  • Update environments by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/107
  • Fix theano lock issue by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/108
  • SpecletSeven SBC by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/111
  • Read count data by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/113
  • Experimentation with a Negative Binomial model by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/115
  • Update data by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/122
  • Mypy updates and other small chores by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/126
  • Revisit Negative Binomial models with re-freshed data by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/130
  • feat: standardize total read counts table col names by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/134
  • Data manager re-write with optional dask backend by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/135
  • style: address code review comments by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/136
  • Speclet eight by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/137
  • Refactor configuration system by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/138
  • SpecletEight fitting by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/141
  • Strict model configuration interface by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/142
  • Build and test SpecletNine model by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/144
  • Refactor modeling system and pipelines for using Stan by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/147
  • Python environment update by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/148
  • Negative binomial models by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/149
  • Larger CRC/Bone subsample by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/150
  • Fix Theano BLAS warning by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/154
  • Add more pieces to the hierarchical negative binomial model by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/157
  • Posterior predictions on new data by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/158
  • Oncogene covariate by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/159
  • Clean by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/160
  • Numpyro PyMC JAX backend by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/162
  • Refactor SLURM resources and run model-fitting pipeline by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/165
  • Data subset with colorectal, pancreas, and esophagus lineages by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/166
  • Attempt at modeling the colorectal, pancreas, and esophageal lineages by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/168
  • Small chores by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/169
  • Address CI of pytest suite by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/171
  • Single lineage model interface by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/172
  • Single lineage model (and some other additions) by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/170
  • GPU support in the model fitting pipeline by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/179
  • Simplify the model to help with sampling by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/176
  • Model version and information by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/185
  • Varying chromosome effects nested under cell line by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/187
  • Update model fitting reports by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/188
  • Expand the analysis to all lineages and sublineages by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/191
  • Figures by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/193
  • Finish up by @jhrcook in https://github.com/Kevin-Haigis-Lab/speclet/pull/196

New Contributors

  • @jhrcook made their first contribution in https://github.com/Kevin-Haigis-Lab/speclet/pull/1

Full Changelog: https://github.com/Kevin-Haigis-Lab/speclet/commits/v1.0.0

- Jupyter Notebook
Published by jhrcook about 3 years ago