{ "cells": [ { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# get the latest version from pypi \n", "# for other installations approaches, see https://dynamo-release.readthedocs.io/en/latest/ten_minutes_to_dynamo.html#how-to-install\n", "!pip install dynamo-release --upgrade --quiet" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let us show that velocity estimation based on slam-seq data gives more consistent and clean results. \n", "Note that this is irrespective of the velocity tools you will use. Original scSLAM-seq authors show that velocyto gives better results when using slam-seq data. Here I am using the same result with the recently improved scvelo package. Please come back to see the result with dynamo! " ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
package | \n", "dynamo-release | \n", "tqdm | \n", "anndata | \n", "cvxopt | \n", "hdbscan | \n", "loompy | \n", "matplotlib | \n", "numba | \n", "numpy | \n", "pandas | \n", "pynndescent | \n", "python-igraph | \n", "scikit-learn | \n", "scipy | \n", "seaborn | \n", "setuptools | \n", "statsmodels | \n", "trimap | \n", "umap-learn | \n", "numdifftools | \n", "colorcet | \n", "
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version | \n", "0.95.0 | \n", "4.48.0 | \n", "0.7.4 | \n", "1.2.3 | \n", "0.8.26 | \n", "3.0.6 | \n", "3.3.0 | \n", "0.48.0 | \n", "1.19.1 | \n", "1.1.0 | \n", "0.4.8 | \n", "0.8.2 | \n", "0.23.1 | \n", "1.5.2 | \n", "0.9.0 | \n", "49.3.1 | \n", "0.11.1 | \n", "1.0.12 | \n", "0.4.3 | \n", "0.9.39 | \n", "2.0.2 | \n", "