{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Preprocessing Tutorial \n", "This tutorial focuses on how to utilize dynamo to preprocess data. In the new version, we make `Preprocessor` class to allow you to freely explore different preprocessing recipes whose step parameters that can be configured inside `Preprocessor`. Existing recipes in preprocessor includes monocle, pearson residual, seurat and sctransform. Moreover, you can replace each preprocessing step with your own implementation with ease. For instance, `Preprocessor`'s monocle pipeline contains `filter_cells_by_outliers`, `filter_genes_by_outliers`, `normalize_by_cells`, `select_genes` and other steps. You can replace the implementation and default monocle parameters passed in to these functions by replacing or changing attributes of `Preprocessor`.\n", "\n", "In older versions, dynamo offer several recipes, among which `recipe_monocle` is a basic function as a building block of other recipes. You can still use these functions to preprocess data. \n", "\n", "`Preprocessor` provides users with `config_monocle_recipe` and other `config_*_recipes` methods to help you reproduce different preprocessor results and integrate with your newly developed preprocessing algorithms." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Import packages" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| package | \n", "umap-learn | \n", "typing-extensions | \n", "tqdm | \n", "statsmodels | \n", "setuptools | \n", "session-info | \n", "seaborn | \n", "scipy | \n", "pynndescent | \n", "pre-commit | \n", "pandas | \n", "openpyxl | \n", "numdifftools | \n", "numba | \n", "networkx | \n", "matplotlib | \n", "loompy | \n", "leidenalg | \n", "igraph | \n", "get-version | \n", "dynamo-release | \n", "colorcet | \n", "anndata | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| version | \n", "0.5.6 | \n", "4.11.0 | \n", "4.66.2 | \n", "0.14.2 | \n", "69.5.1 | \n", "1.0.0 | \n", "0.13.2 | \n", "1.11.4 | \n", "0.5.12 | \n", "3.7.1 | \n", "1.5.3 | \n", "3.1.4 | \n", "0.9.41 | \n", "0.58.1 | \n", "3.3 | \n", "3.9.2 | \n", "3.0.7 | \n", "0.10.2 | \n", "0.10.8 | \n", "3.5.5 | \n", "1.4.2rc1 | \n", "3.1.0 | \n", "0.10.7 | \n", "