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v0.2.2 (2020-06-22)

  • Added abilitiy to import/export expression data from/to Scanpy (see new tutorial!).

    • ExpMatrix.from_anndata() imports an AnnData object (Scanpy)
    • Conversely, matrix.to_anndata() exports the expression matrix as an AnnData object.

  • Added utility function util.zscore() to convert a matrix to z-scores.

v0.3.0 (2021-05-14)

  • Added support for heatmaps (workflows.overexpressed_gene_heatmap())

  • Improved data preprocessing (preprocess.preprocess_data()) that allows better reporting of QC metrics

  • Support for graph-based clustering using the Leiden algorithm, by running Scanpy's implementation using the Monet latent space model (workflows.graph_based_clustering())

  • Latent space model simplified => Now everything is built around the PCAModel class

  • Nearest-neighbor aggregation function optimized (now uses scikit-learn NearestNeighbor class)

  • Support for processing data produced with STARsolo's Velocyto option

  • New concepts of workflows that provide a simplified API to streamline common analysis tasks (try from monet import workflows as flow), including:

    • Data preprocessing (e.g., workflows.preprocess_10x_v3())
    • Visualization (e.g., workflows.tsne())
    • Clustering (e.g., workflows.graph_based_clustering())