Recent Releases of inferelator
inferelator - Inferelator v0.6.3
Inferelator v0.6.3 July 8, 2024
Bug Fixes:
Removed import-time setting environment variables for threading control. Threading is now handled directly by parallelization (e.g. through joblib).
Updated code to address breaking changes in Numpy 2.0.0 and Scipy 1.14.0
- Python
Published by asistradition over 1 year ago
inferelator - v0.6.1
Inferelator v0.6.1 January 3, 2023
New Functionality:
- Extended support for mRNA velocity & decay calculations
- Added new experimental TFA modules
Code Refactoring:
- Workflow, ResultProcessor, and InferelatorData restructured for readability and clearer commenting
Bug Fixes:
- Slicing individual gene data returns numpy vector instead of anndata view
- Corrected several deprecated pandas calls to eliminate FutureWarnings
- Python
Published by asistradition about 3 years ago
inferelator - v0.6.0
Inferelator v0.6.0 September 14, 2022
New Functionality:
- Support for grouping arbitrary genes from multiple tasks into learning groups
- Workflow to learn homology groups together
- Workflow to explicitly incorporate velocity and decay into learning
- Added support for batching parallelization calls to reduce overhead when data is relatively small
Code Refactoring:
- Refactored multi-task learning to parameterize tfs and genes for each task
- Refactored parallelization around joblib & dask
- Removed pathos and replaced with joblib
- Optimized StARS-LASSO by replacing standalone LASSO with lasso_path
Bug Fixes:
- Fixed several messages to be more informative
- usenoprior is appropriately applied in multitask learning
- Python
Published by asistradition over 3 years ago
inferelator - v0.5.8
Bug Fixes:
- Corrected combining multi-task gene and tf labels
- Python
Published by asistradition almost 4 years ago
inferelator - v0.5.7
New Functionality:
- Added support for numba acceleration of AMuSR with
.set_run_parameters(use_numba=True)(PR #46)
Code Refactoring:
- Updated example scripts
- Removed deprecated KVS multiprocessing and associated code
Bug Fixes:
- Gene labels are included as the first column of the produced confidences TSV file by default
- Matplotlib backend selection checks for non-interactive mode
- Python
Published by asistradition over 4 years ago
inferelator - v0.5.6
Inferelator v0.5.6 August 16, 2021
New Functionality:
- Added code to randomly generate noise in prior with
.set_shuffle_parameters(add_prior_noise=None) - Added in-workflow benchmarks for CellOracle and pySCENIC
Code Refactoring:
- Minor changes to matplotlib interface
- Improved testing for multitask workflows
- Improved error messaging around prior and gold standard
- Switch from Travis.ci to GitHub Actions for continuous integration
- Python
Published by asistradition over 4 years ago