Built on Decima (Lal et al., 2024) and ZebraHub (Lange et al., 2024). The 16 checkpoints in this deposit correspond to the systematic experiments enumerated in daniodecima-applications-main/notebooks/4_evaluation/ckpt_dirs_celltypes.txt in the accompanying code archive.
", "type": { "id": "notes", "title": { "de": "Anmerkungen", "en": "Notes" } } } ], "contributors": [ { "affiliations": [ { "name": "Chan Zuckerberg Biohub San Francisco" } ], "person_or_org": { "family_name": "Senbabaoglu", "given_name": "Yasin", "name": "Senbabaoglu, Yasin", "type": "personal" }, "role": { "id": "contactperson", "title": { "de": "Kontaktperson", "en": "Contact person" } } }, { "affiliations": [ { "name": "Chan Zuckerberg Biohub San Francisco" } ], "person_or_org": { "family_name": "Royer", "given_name": "Loic A.", "name": "Royer, Loic A.", "type": "personal" }, "role": { "id": "contactperson", "title": { "de": "Kontaktperson", "en": "Contact person" } } } ], "creators": [ { "affiliations": [ { "name": "Chan Zuckerberg Biohub San Francisco" } ], "person_or_org": { "family_name": "Voges", "given_name": "Mathias J.", "name": "Voges, Mathias J.", "type": "personal" } }, { "affiliations": [ { "name": "Chan Zuckerberg Biohub San Francisco" } ], "person_or_org": { "family_name": "Kim", "given_name": "Yang Joon", "name": "Kim, Yang Joon", "type": "personal" } }, { "affiliations": [ { "name": "Chan Zuckerberg Biohub San Francisco" } ], "person_or_org": { "family_name": "Frank", "given_name": "Max", "name": "Frank, Max", "type": "personal" } }, { "affiliations": [ { "name": "Chan Zuckerberg Biohub San Francisco" } ], "person_or_org": { "family_name": "Iovino", "given_name": "Ben", "name": "Iovino, Ben", "type": "personal" } }, { "affiliations": [ { "name": "Chan Zuckerberg Biohub San Francisco" } ], "person_or_org": { "family_name": "Senbabaoglu", "given_name": "Yasin", "name": "Senbabaoglu, Yasin", "type": "personal" } }, { "affiliations": [ { "name": "Chan Zuckerberg Biohub San Francisco" } ], "person_or_org": { "family_name": "Royer", "given_name": "Loic A.", "name": "Royer, Loic A.", "type": "personal" } } ], "description": "DanioDecima is a deep-learning framework for predicting\nsingle-cell RNA-seq expression directly from genomic DNA sequence in zebrafish\ndevelopment. It extends the Decima\narchitecture (a Borzoi-based sequence-to-expression model) by fine-tuning on the\nZebraHub single-cell developmental atlas.
\n\nThis deposit contains:
\nv0.1.0-preprint (commit edf3fdc) as a tar.gz archive.last.ckpt) covering the four\n initialization strategies (Human-Decima, Human-Borzoi, Mouse-Borzoi, Random) \u00d7 4 replicates\n each \u2014 the systematic experiments described in the accompanying manuscript.See MANIFEST.md in this deposit for the per-file index and loading instructions.
License: this work is a derivative of\nGenentech/decima and inherits the\nGenentech Non-Commercial Software License v1.0 \u2014 commercial use\nprohibited. The full license text is at the top of the code archive\n(LICENSE.md and daniodecima-main/LICENSE.txt). The Zenodo\nlicense metadata field is set to \"Other (non-commercial)\" because the Genentech\nNC v1.0 is not in Zenodo's controlled vocabulary; the LICENSE.md inside the\narchive is the authoritative legal text.
Citation: see the README in the code archive for BibTeX entries\ncovering Decima (Lal et al., 2024), ZebraHub (Lange et al., 2024), and DanioDecima.
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