https://github.com/kuleshov-group/genomics-lrb-viztool
Visualization of results on Genomics Long-Range Benchmark by annotations
Science Score: 21.0%
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Organization kuleshov-group has institutional domain (www.cs.cornell.edu) -
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○Scientific vocabulary similarity
Low similarity (7.4%) to scientific vocabulary
Repository
Visualization of results on Genomics Long-Range Benchmark by annotations
Basic Info
- Host: GitHub
- Owner: kuleshov-group
- Language: Python
- Default Branch: main
- Size: 7.07 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Analyzing results of Genomics LRB Benchmarking
Use the notebook lrb_results_analysis.ipynb to analyze results of the initial model benchmarking; slice results by distances to transcription start sites (TSS) and different annotations (e.g., promoter, enhancer, intron/exon, etc.).
Getting started
Step 1: Clone this repository:
bash
git clone git@github.com:kuleshov-group/genomics-lrb-viztool.git
cd genomics-lrb-viztool
Step 2: Create conda env and install requirements:
bash
conda create -n lrb_env python=3.10
conda activate lrb_env
pip install -r requirements.txt
Step 3: Download and unzip results files from the HF dataset:
bash
wget -O results_with_annotations.zip https://huggingface.co/datasets/InstaDeepAI/genomics-long-range-benchmark/resolve/main/results_with_annotations.zip?download=true
unzip results_with_annotations.zip
Start the notebook server and use this notebook lrb_results_analysis.ipynb:
bash
jupyter notebook
Run all cells.
Use the widgets to analyze different tasks by various splits.
Owner
- Name: Kuleshov Group @ Cornell Tech
- Login: kuleshov-group
- Kind: organization
- Website: https://www.cs.cornell.edu/~kuleshov/
- Twitter: volokuleshov
- Repositories: 7
- Profile: https://github.com/kuleshov-group
Research group at Cornell focused on machine learning, generative models, AI for science
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Dependencies
- gdown *
- ipdb *
- ipython *
- ipywidgets *
- matplotlib *
- notebook *
- numpy *
- pandas *
- scikit-learn *
- seaborn *
- tqdm *