de Boer Lab @ UBC
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CisRegModels
CisRegModels PublicScripts for building computational models of gene regulation with tensorflow
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Genomic-API-for-Model-Evaluation
Genomic-API-for-Model-Evaluation PublicGAME was designed for the functional genomics community to create seamless communication across pre-trained models and genomics datasets. It is a product of the feedback from many model and dataset…
Repositories
- dna_active_learning Public
de-Boer-Lab/dna_active_learning’s past year of commit activity - GAME-CpG-predictor Public
CpG predictor serves as a baseline for models which are correlated with many genomic readouts. It ignores the type, cell type and species keys in the Evaluator requests since it is simply counting CpG instances.
de-Boer-Lab/GAME-CpG-predictor’s past year of commit activity - GAME-consistency-evaluators Public
To evaluate whether models were internally consistent in their predictions, we created Consistency Evaluators.
de-Boer-Lab/GAME-consistency-evaluators’s past year of commit activity - Genomic-API-for-Model-Evaluation Public
GAME was designed for the functional genomics community to create seamless communication across pre-trained models and genomics datasets. It is a product of the feedback from many model and dataset experts and our hope is that it allows for long-lasting benchmarking of models.
de-Boer-Lab/Genomic-API-for-Model-Evaluation’s past year of commit activity - GAME_matcher Public
de-Boer-Lab/GAME_matcher’s past year of commit activity - GAME-predictor-distributor Public
The creation of massive genomics datasets will continue to increase rapidly and thus to further future proof GAME’s utility we designed Predictor Distributor (PD). PD is an optional module that acts as a transparent orchestration layer implementing a scatter-gather design.
de-Boer-Lab/GAME-predictor-distributor’s past year of commit activity - GAME_modules Public
de-Boer-Lab/GAME_modules’s past year of commit activity - GAME-Borzoi-Enformer-TestSet-track-evaluator Public
As most of the sample Evaluators request point-based predictions, we incorporated an Evaluator that explicitly requests and evaluates track-based predictions. To construct this Evaluator, we intersected and merged genomics coordinates from the Enformer and Borzoi test datasets.
de-Boer-Lab/GAME-Borzoi-Enformer-TestSet-track-evaluator’s past year of commit activity - GAME-Martyn-variant-effects-evaluator Public
Martyn et al. dataset measured the effects of 783 variants in Jurkat T cells and THP-1 monocytes cells. This Evaluator is used to evaluate models' abilities to predict variant effects. We extract 2000bp around the indel and request log scale expression predictions for the reference and mutated sequence.
de-Boer-Lab/GAME-Martyn-variant-effects-evaluator’s past year of commit activity
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