Notebook readme#2

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RevathyVenukuttan wants to merge 26 commits into

bmajoros:mainfrom

Duke-IGVF:notebook_readme

Commits on May 15, 2024

Adds python dependencies in standard requirements format
hlapp
committed

Commits on May 21, 2024

Merges changes from upstream (bmajoros/BlueSTARR)
hlapp
committed

Commits on Jun 25, 2024

Merge changes from upstream (bmajoros/BlueSTARR)
hlapp
committed

Commits on Jun 27, 2024

Adds conda environment definition
hlapp
committed

Commits on Aug 28, 2024

Add dockerfile for building BlueSTARR images (#4)
tncowart
authored

Commits on Sep 3, 2024

Adds GitHub Action workflow to automatically build Docker image
hlapp
committed

Commits on Nov 1, 2024

Commits on Nov 2, 2024

Commits on Jan 16, 2025

BlueSTARR version used for v0.1.1 model training

yutiachen5
authored and
hlapp
committed

Commits on May 13, 2025

Clarifies instructions for building conda environment
hlapp
committed

Commits on Jul 6, 2025

Adds sequence index to true-vs-predicted table

authored and
hlapp
committed

Commits on Jul 7, 2025

Allows loading pretrained weights prior to training
hlapp
committed

Commits on Sep 2, 2025

Commits on Sep 8, 2025

Adds library size normalization for custom loss (#15)

hlapp
and
bmajoros
authored

Commits on Sep 30, 2025

Fixed library size ratio calculation
hlapp
committed

Commits on Dec 3, 2025

Updates transformer-based model architecture
hlapp
committed

Commits on Mar 23, 2026

Commits on Mar 24, 2026

Adds documentation and links for downsampling
hlapp
committed

Commits on Mar 25, 2026