Benchmark for Splice Models

• SpliceAI
• SegmentNT
• Pangolin
• SpliceTransformer

Setup environment

singularity build env/splice-benchmark.sif docker://clarity001/bioinformatics:splice-benchmark
singularity shell --nv --bind /zata,/data env/splice-benchmark.sif

uv sync

uv add axial-positional-embedding sinkhorn-transformer transformers spliceai gtfparse git+https://github.com/instadeepai/nucleotide-transformer@main git+https://github.com/tkzeng/Pangolin.git@main