Monet

Latest version: v0.3.2

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0.3.0

* 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()`)

0.2.2

* 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.

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