Pegasus for Single Cell Analysis

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Pegasus is a tool for analyzing transcriptomes of millions of single cells. It is a command line tool, a python package and a base for Cloud-based analysis workflows.

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Release Highlights in Current Stable

1.2.0 December 25, 2020

  • tSNE support:

    • tsne function in API: Use FIt-SNE for tSNE embedding calculation. No longer support MulticoreTSNE.

    • Determine learning_rate argument in tsne more dynamically. ([Belkina19], [Kobak19])

    • By default, use PCA embedding for initialization in tsne. ([Kobak19])

    • Remove net_tsne and fitsne functions from API.

    • Remove --net-tsne and --fitsne options from pegasus cluster command.

  • Add multimodal support on RNA and CITE-Seq data back: --citeseq, --citeseq-umap, and --citeseq-umap-exclude in pegasus cluster command.

  • Doublet detection:

    • Add automated doublet cutoff inference to infer_doublets function in API. ([Li20-2])

    • Expose doublet detection to command-line tool: --infer-doublets, --expected-doublet-rate, and --dbl-cluster-attr in pegasus cluster command.

    • Add doublet detection tutorial.

  • Allow multiple marker files used in cell type annotation: annotate function in API; --markers option in pegasus annotate_cluster command.

  • Rename pc_regress_out function in API to regress_out.

  • Update the regress out tutorial.

  • Bug fix.