May 11, 2019. Oct 03, 2019. Uncheck both checked options and click on Finish button, and your Anaconda installation is complete. Now, let’s access Anaconda Prompt. Go to Search/Run and type Anaconda Prompt and hit enter. A black window like below will open. This is Anaconda Prompt. We will now start jupyter notebook from anaconda prompt.
To visualize the cell clusters, there are a few different dimensionality reduction techniques that can be helpful. The most popular methods include t-distributed stochastic neighbor embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP) techniques.
In the Seurat package there is a function to use the UMAP visualization (
RunUMAP() ), however it does require the user to first install the umap-learn python package. To install this package follow the instructions below.
These materials were modified from https://unidata.github.io/online-python-training/conda-windows.html.
The aim of this web page is to help you get started with Python. We will explain what a package management tool is, how to download
conda package management tool via the Anaconda installer, and guide you on the Mac/Windows command prompt so that you can use conda from the command line. Finally, we will wrap up by installing one library with conda .
What Is a Package Management Tool?
A package management tool is a software application that helps you manage software libraries that enable you to get your work done. These software libraries may relate to plotting for scientific publication or accessing certain kinds of data, for example.
When you start using Python, you will want use software libraries that are not part of the standard Python installation. For example, we wish to use the umap-learn for cluster visualization. Anaconda from Continuum Analytics will help you install
umap-learn easily.
Installing the
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December 2020
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