Code

Reference mapping#77

Code

Merged

subercui merged 33 commits intomainbowang-lab/scGPT:mainfrom reference-mappingbowang-lab/scGPT:reference-mappingCopy head branch name to clipboardSep 6, 2023

Commits

Commits on Aug 25, 2023

• 🍱 add reference mapping notebook

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  40938e8

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• 🎨 update ref map atlas notebook

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• 🎨 update ref map atlas notebook

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Commits on Aug 26, 2023

• 🍱 add build atlas index

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Commits on Aug 30, 2023

• 🍱 add build atlas index faiss

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Commits on Aug 31, 2023

• 🎨 update build atalas index faiss

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• 🍱 add test faiss

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• 🎨 update index factory info in build atlas faiss

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• 🎨 update nprobe setting in test faiss

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  34a9aba

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• 🎨 update default index factory, and auto set nprobe

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• 🎨 update variable name

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• 🎨 update load index in build atlas index

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Commits on Sep 1, 2023

• 🎨 update load index function

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  a7fd633

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• 🚚 rename and update build atlas index faiss

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  97a1251

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• 🎨 update variable names and read files in atlas index faiss

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  912473c

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• 🔧 fix loading data

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• 🎨 rename variables and update nprobe setting

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Commits on Sep 3, 2023

• 🎨 update reference mapping atlas

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• 🎨 update build atlas index and ref mapping notebook

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Commits on Sep 4, 2023

• ✨ add get cell emb in tasks and update scripts

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• 🎨 update model

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• 🎨 update notebooks

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• 🎨 update load meta labels

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• ✨ add embed data in tasks

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• ✨ add embed atlas

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• 🎨 refactor preprocess

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  54c203d

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• 🎨 update ref map notebook

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  a712bed

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Commits on Sep 5, 2023

• 🎨 update cell emb

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  684caa4

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• 🎨 update and run embed atlas

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  6f6ae1d

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• 🚚 move and rename files

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• 🎨 update build atlas index faiss

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  2664354

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Commits on Sep 6, 2023

• 🎨 update tutorial reference mapping

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  28f469d

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• clear files

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