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Cui et al. |

scGPT: Reference Mapping Using Cell Embedding

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Genomics & Multi-Omics
Step 1: Upload your data

Upload Single Cell RNA-Seq Data File

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  • Your file can be in the following formats:h5ad
    • The h5ad format in scRNA-seq refers to the Hierarchical Data Format 5 (HDF5) Annotated Data format. It is commonly used to store single-cell gene expression data.
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Step 2: Set Parameters
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Efficiently map your data with the scGPT_human model. Leverage pre-trained embeddings in a zero-shot setting for quick, accurate cell analysis. Ideal for transferring cell type and disease condition metadata, this tool simplifies understanding cell compositions in new samples.

Example use case: Understand the cell composition of newly collected samples.

Technology: Transformers,

Limitations:  
  • Please note that the reference mapping is a new experimental feature.
  • Some of the parameters are kept as default please see the reference tutorial.
Citation:
scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI Haotian Cui, Chloe Wang, Hassaan Maan, Kuan Pang, Fengning Luo, Bo Wang bioRxiv 2023.04.30.538439; doi: https://doi.org/10.1101/2023.04.30.538439.
Released:
Nov-06-2023
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