Basenji
Basenji is an open source tool for predicting the effect of genomic variants on transcription using deep learning. It's optimized for accuracy and runs quickly on a personal computer.
genomics
deep-learning
transcription
variant-effect-prediction
Basenji: Open Source Genomic Variant Prediction Tool
Basenji is an open source tool for predicting the effect of genomic variants on transcription using deep learning. It's optimized for accuracy and runs quickly on a personal computer.
What is Basenji?
Basenji is an open-source machine learning software for predicting the effects of genomic variants on gene expression and transcription. It utilizes deep neural networks trained on a large database of variants to accurately predict expression changes from DNA sequences.
Some key features and capabilities of Basenji include:
- High accuracy in predicting expression changes from SNPs, indels, and larger structural variants
- Rapid prediction on a personal computer - full chromosome analysis takes just a few minutes
- Quantifies the effect of variants on both proximal and distal transcription
- Open source Python implementation leveraging Tensorflow and Keras
- Pre-trained models available for human and mouse genomes
- Custom model training support for other organisms or cell types
- Active development and user community support
Basenji represents the state-of-the-art in predicting transcriptional regulation from DNA sequence. Its accuracy and speed make it valuable for studying disease-causing variants, functional genomics, and Precision Medicine applications.
Basenji Features
Features
- Uses deep learning to predict effects of variants on transcription
- Optimized for accuracy
- Runs quickly on a personal computer
- Open source and freely available
Pricing
- Open Source
Pros
Accurate predictions
Fast performance
Easy to use
Free and open source
Cons
Requires some bioinformatics expertise
Limited to predicting transcriptional effects
May require significant compute resources for training models
Official Links
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