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

1.9.1 March 16, 2024

New Feature

Improvement

  • For dotplot function, add show_only_expressed parameter to decide whether the color intensity of dots are based on cells expressing the genes to show or all cells. By default, show_only_expressed=True. (PR 292)

  • Allow scatter and spatial functions to have a list of vmin and vmax values when plotting multiple features.

  • For scatter, spatial, dotplot, violin functions, when some features are not in the data, emit a warning message and continue with features existing in the data.

  • In spatial function, add nrows and ncols to organize subplots.

  • In calculate_z_score function, enforce the input count matrix to be dense or scipy.csr_matrix.

  • In plot_gsea function, add label_fontsize parametere to allow change font label size in GSEA plots.

1.9.0 January 19, 2024

New Feature and Improvement

  • calculate_z_score works with sparse count matrix. [PR 276 Thanks to Jayaram Kancherla]

  • Plotting functions (scatter, dotplot, violin, heatmap) now give warnings on genes/attributes not existing in the data, and skip them in the plots.

  • Improve heatmap:

    • Add show_sample_name parameter for cases of pseudo-bulk data, nanoString DSP data, etc.

    • Use Scipy’s linkage (scipy.cluster.hierarchy.linkage) for dendrograms to use its optimal ordering feature for better results (see groupby_optimal_ordering parameter).

  • Update human lung and mouse immune markers used by infer_cell_types function.

  • run_harmony can accept multiple attributes to be the batch key, by providing a list of attribute names to its batch parameter.

  • Expose online_batch_size parameter in nmf and integrative_nmf functions.