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R is a programming language. To use R, we need to install an Integrated Development Environment (IDE).Rstudio is the Best IDE available as it is user-friendly, open-source and is part of the Anaconda platform. Filename Size Last Modified MD5; Anaconda3-2020.07-Linux-ppc64le.sh: 290.4M: 2020-07-23 12:16:47: daf3de1185a390f435ab80b3c2212205: Anaconda3-2020.07-Linux-x8664.sh. Instead, use Anaconda software by opening Anaconda Navigator or the Anaconda Prompt from the Start Menu. Choose whether to register Anaconda as your default Python. Unless you plan on installing and running multiple versions of Anaconda or multiple versions of.
Review this page to learn what Anaconda Navigator is. When you’re ready tostart working in Navigator, check out the user guide topics:
Overview | Installation | Glossary | Getting started with Navigator | Tutorials | Troubleshooting | Release notes | Help and support
Installing Navigator¶. Navigator is automatically installed when you install Anaconda version 4.0.0. Conda install -c anaconda spyder Description Spyder is a powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.
What is Anaconda Navigator?¶
Anaconda Navigator is a desktop graphical user interface (GUI)included in Anaconda® distribution that allows you to launch applicationsand easily manage conda packages, environments, and channels without usingcommand-line commands. Navigator can search for packages on Anaconda Cloudor in a local Anaconda Repository. It is available for Windows, macOS, andLinux.
To get Navigator, get the
NavigatorCheatSheet
and install Anaconda.The Getting started with Navigator section shows how to start Navigator from theshortcuts or from a terminal window.
Why use Navigator?¶
In order to run, many scientific packages depend on specific versions of otherpackages. Data scientists often use multiple versions of many packages anduse multiple environments to separate these different versions.
The command-line program conda is both a package manager and an environmentmanager. This helps data scientists ensure that each version of each packagehas all the dependencies it requires and works correctly.
Navigator is an easy, point-and-click way to work with packages andenvironments without needing to type conda commands in a terminalwindow. You can use it to find the packages you want, install them inan environment, run the packages, and update them – all inside Navigator.
What applications can I access using Navigator?¶
The following applications are available by default in Navigator:
- Anaconda Prompt (Windows only)
- Anaconda PowerShell (Windows only)
Advanced conda users can also build their own Navigator applications.
How can I run code with Navigator?¶
The simplest way is with Spyder. From the Navigator Home tab, click Spyder,and write and execute your code.
You can also use Jupyter Notebooks the same way. Jupyter Notebooks are anincreasingly popular system that combine your code, descriptive text, output,images, and interactive interfaces into a single notebook file that is edited,viewed, and used in a web browser.
Navigator user guide¶
Note
We do not support macOS<10.12 for Anaconda Navigator.
Format
The workshop consists of explanatory discussions interspersed with hands-on exercises. We strongly encourage you to bring a laptop with all required packages installed in order to fully participate. We will also have office hours with CZI computational biology staff available in the morning to help troubleshoot any installation issues before class begins.
Installation guide (before class)
1. Install Python via Anaconda
Even if you have previously installed Python, please install Anaconda for Python version 3 (available on OSX, Linux, and Windows). You can simply click through the install wizard (no customization required, all the defaults are fine).
Anaconda is package manager, which means that it helps coordinate your Python installation and related packages (useful code written by other people for performing specific tasks) for you so that you have a consistent environment (the version of Python and the version of the code in each package that your computer looks at when doing your analysis).
You should now see an icon for 'Anaconda Navigator' in your Applications folder (mac) or the Start menu (Windows). Please contact the instructors if you do not see this icon!
2. Install required packages (for Mac OS)
2A. Install Bioconda
Not everyone who uses Anaconda is a biologist. As a result, some biology-specific packages are only available in the Bioconda channel (collection of packages).
- Open Anaconda Navigator.
- Click on
Environments
in the left sidebar - Click on
Channels
in the top middle of the screen - Click on
Add..
- In the bottom text box, type
bioconda
and pressEnter
- Press
Update channels
2B. Download the course config file
To handle installation of all the Python packages required for the workshop (both days, all tracks), we have prepared a configuration file that tells Anaconda how to configure your environment.
- Download the configuration file called
sfn-workshop-mac.yml
here. Save it an a spot you'll remember. - Open Anaconda Navigator
- Click on
Environments
in the left sidebar - Click on
Import
in the bottom left - Enter
sfn-workshop
as the Name, and browse for thesfn-workshop-mac.yaml
file you just downloaded - Press
Import
2. Install required packages (for windows)
2A. Download the course config file
To handle installation of all the Python packages required for the workshop (both days, all tracks), we have prepared a configuration file that tells Anaconda how to configure your environment.
- Download the configuration file called
sfn-workshop-windows.yml
here. Save it an a spot you'll remember. - Open Anaconda Navigator
- Click on
Environments
in the left sidebar - Click on
Import
in the bottom left - Enter
sfn-workshop
as the Name, and browse for thesfn-workshop-windows.yaml
file you just downloaded - Press
Import
2B. Install scanpy (for Windows users in the single-cell track only)
- Click on the green play button next to the
sfn-workshop
and choose 'Open terminal' - Enter
python3 -m pip install scanpy
and pressEnter
3. Check your installation
- Open Anaconda Navigator
- Click on
Environments
in the left sidebar - Select the
sfn-workshop
environment from the list. This may take several minutes. - Click on the green
play
button that appears - Select
Open with Jupyter Notebook
from the list
You should get a browser tab that says 'Jupyter' at the top and lists all the files on your computer. This might not seem like much, but is all you need to get started! :)
Install Anaconda Navigator Mac
If this does not work, please come to office hours before class so the CZI computational biology team can help you
4. Download course files
For the imaging track
Go to https://github.com/sofroniewn/2019-ndcn-comp-bio-imaging
For the single cell track
Go to https://github.com/chanzuckerberg/scRNA-python-workshop
Anaconda Navigator Download Windows
Clone or download contents
If you are comfortable cloning a repository with git, we encourage you to do so. Otherwise, click the green 'clone or download' button and choose 'download zip'. We encourage you to do this the evening before class, as we may make some last-minute updates to the material.
5. Bonus: install fun visualization tools (optional)
- Open a terminal window (Mac: Applications > Utilities > Terminal; Windows: Start > Windows System > Command Prompt)
For the imaging track:
- In the terminal window, copy and paste the following and press
Enter
:http://www.alexunco1977.simpsite.nl/splinter-cell-blacklist-costume. Archer and Kestrel have a smaller body type compared to Fisher, as well as minor appearance changes between the two.python3 -m pip install napari
To test your installation of napari, type
napari
in the next terminal line and press Enter
. You should see an application window open up.For the single-cell analysis track:
- In the terminal window, copy and paste the following and press
Enter
:python3 -m pip install cellxgene
To test your installation of cellxgene, type
cellxgene
in the next terminal line and press Enter
. You should see something like this:Usage: cellxgene [OPTIONS] COMMAND [ARGS].. Options: --version Show the version and exit. --help Show this message and exit. Commands: launch Launch the cellxgene data viewer. prepare Preprocesses data for use with cellxgene.