Releases: auerbachs/BMDExpress-3
Releases · auerbachs/BMDExpress-3
BMDExpress 3.20.0106
New Features
- Added venn diagram visualizations to category analysis and BMD analysis results viewers.
- Add upstream analysis notes to exported files.
Bug Fixes
- Fixed an issue flagging hill models when BMD is below the lowest dose. Previously the application interpreted 1/3 as 1/4 and 1/2 as 1/3 due to a bug creating the flag hill ratio value.
BMDExpress 3.20.0095
New Features
- Add Adverse Direction (dose-response curve direction of response) filter to Category Analysis to allow for gene set analysis of up- or down-regulated genes in isolation.
- Update labels in Category Analysis input view to be consistent and explicit
- To help with empirical false discovery analysis the total possible geneset counts for a data set based on platform annotation and gene set size filter were added to the Category Analysis notes.
Bug Fixes
- Fixed issue causing Polynomial models to produce non-monotonic results when user specified monotonic restriction
BMDExpress 3.20
New Features
- R-squared (coefficient of determination) as an alternative to global goodness of fit p-value for evaluating fit of models to data
- Step Function detection with user defined thresholds for application to modeled curves to facilitate identification and removal of biologically implausible responses
- Export fitted curve response data
- Add category analysis filter parameters
- Predefine the Min/Max number of genes in gene set
- Remove fits that are step functions
- Remove fits that are step functions with BMD less than lowest dose
- Filter fitted responses based on R-squared
Bug Fixes
- Fixed issue when running multiple One Way ANOVA analyses causing LOTEL/NOTEL
calculation to shuffle p-value and fold change parameters in GUI. This was not an issue when running one dataset at a time and in the command line version - Fixed issue cause by invalid default folder path for exporting and importing data.
BMDExpress 3.1
- Enable relative deviation during BMD Analysis for non-log transformed data
- QC Bar chart for expression data to show gene expression direction per dose based on T-Test
- Polynomial 2 model now has option to be non-monotonic
- Add polynomial 2 model to curve fit prefilter
- Add ability to save curve fit prefilter settings
BMDExpress 3
- Laplace and MCMC Bayesian model averaging (based the approach used in ToxicR package -- https://github.com/NIEHS/ToxicR)
- Curve fit-based prefilter to identify dose responsive features more effectively
- New maximum likelihood estimate models currently employed EPA's BMDS software for best model-based approaches
- Alternative confidence interval estimate method (Wald) that allows for more rapid curve fitting
- Forward toxicokinetic modeling to estimate internal dose levels based upon external dose BMD value