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Cui et al. |

scGPT: Mapping

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Omics
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Step 1: Upload your data

Upload Single Cell RNA-Seq Data File

Drag your file(s) or upload
  • 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.
or
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Step 2: Set Parameters
Step 3: Complete run profile
Where to save results?

Default. Save in a secure and encrypted S3 bucket in our infra.

Mounting lets you access files from your S3 for running jobs and save job results directly to it.

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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