de Boer Lab @ UBC
Popular repositories Loading
-
-
CisRegModels
CisRegModels PublicScripts for building computational models of gene regulation with tensorflow
-
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
- 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_modules Public
de-Boer-Lab/GAME_modules’s past year of commit activity - GAME-Enformer-predictor Public
The Enformer module encapsulates the human head of the large-scale multi-task Enformer model and can make predictions for sequences of any length. Its training data includes chromatin accessibility, DNA binding and expression.
de-Boer-Lab/GAME-Enformer-predictor’s past year of commit activity - GAME-ChromBPNet-predictor Public
The ChromBPNet Predictor encapsulates 9 individual chromatin accessibility models (5 folds for each model, some trained with ATAC-seq data and others with DNase) across five cell types.
de-Boer-Lab/GAME-ChromBPNet-predictor’s past year of commit activity - position-mpra Public
Variant Position Modulates Functional Impact in Massively Parallel Reporter Assays
de-Boer-Lab/position-mpra’s past year of commit activity - GAME-Orca-evaluator Public
We designed three Evaluators requesting H1 cell interaction matrices for Chr 8/9 (Orca test set) and Chr 10 (validation set). They tile chromosomes in 1Mb steps, extracting hg38 sequences at runtime. Evaluation computes Pearson correlations between predicted and measured Hi-C matrices. These modules also demonstrate msgpack-numpy response support.
de-Boer-Lab/GAME-Orca-evaluator’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-Gosai-synthetic-MPRA-evaluator Public
This synthetic MPRA (Gosai et al. 2024) Evaluator requests expression predictions for ~51k synthetic probes in K562 (erythroid precursors), HepG2 (hepatocytes) and SK-N-SH (neuroblastoma). The Pearson r is calculated between the measured and predicted log2FC values.
de-Boer-Lab/GAME-Gosai-synthetic-MPRA-evaluator’s past year of commit activity - nextFrag Public
A PyTorch-based framework for benchmarking active learning strategies on DNA sequence-to-expression models.
de-Boer-Lab/nextFrag’s past year of commit activity - hashFrag Public
A command-line tool to mitigate homology-based data leakage in sequence-to-expression models
de-Boer-Lab/hashFrag’s past year of commit activity
People
This organization has no public members. You must be a member to see who’s a part of this organization.
Top languages
Loading…
Most used topics
Loading…