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Introduction to Python for HDC
====
URL to this page: https://hackmd.io/s/rkDieDyoE
**Sign in to each class meeting** [here](https://goo.gl/forms/j4MbWJuPoIYeJET12)
**Software:** This class uses Jupyter notebooks to run Python code. Please see [this page](https://github.com/fredhutchio/fredhutch.io/blob/gh-pages/software.md#python) for instructions to install Anaconda, which will provide Python, Jupyter notebooks, and other packages we'll use for this course. Please note that you do NOT need to install plotnine (we'll be using week 4 for machine learning instead).
This page is for easy access to links we'll use during class. You don't need to do anything with this information until directed by your instructor. Links to the instructor's script will be added as the course progresses.
If you have feedback about this course, please [comment here](https://goo.gl/forms/Bw8dTV0Wghq2iG5i2)
Complete class notes [here](https://github.com/fredhutchio/python_intro_hdc), although note that we will replace week 4 material with machine learning instead.
**Week 1: Intro to Python and Jupyter Notebooks**
* [example notebook](https://github.com/rasilab/machkovech_2018/blob/master/scripts/NA43_competition.ipynb)
* [python style guide](https://www.python.org/dev/peps/pep-0008/)
* [glossary of Python terms](https://www.codecademy.com/articles/glossary-python)
* Instructor's notebook (note: you will need to download this script and put in your project directory)
* [link]()
**Week 2: Working with data**
* URL for direct download into R from GitHub: https://raw.githubusercontent.com/fredhutchio/R_intro/master/extra/clinical.csv
* Other example data files:
example1: https://raw.githubusercontent.com/fredhutchio/R_intro/master/extra/clinical.tsv
example2: https://raw.githubusercontent.com/fredhutchio/R_intro/master/extra/clinical.txt
* [Zipped data file](https://www.dropbox.com/s/k639bkse64r0bfz/data.zip): download, unzip, add three files to data/ in project directory
* [Pandas cheatsheet](https://github.com/pandas-dev/pandas/raw/master/doc/cheatsheet/Pandas_Cheat_Sheet.pdf)
* Instructor's notebook (note: you will need to download this script and put in your project directory)
* [link]()
**Week 3: Extracting data from data frames**
* [matplotlib documentation](https://matplotlib.org)
* Instructor's notebook (note: you will need to download this script and put in your project directory)
* [link]()
**Week 4: Machine learning**
* see [slides](https://github.com/fredhutchio/python_intro_hdc/blob/master/slides/Intro%20to%20Machine%20Learning.pptx) and [notebooks](https://github.com/fredhutchio/python_intro_hdc/tree/master/notebooks)
**Resources for continued learning**
* The original Intro to Python course includes a section on data visualization with the package plotnine (which implements ggplot). The [materials](https://github.com/fredhutchio/python_intro/blob/master/week4.py) should be fairly straightforward to work through on your own, if you are interested.
* We are currently pilot testing a new course, intermediate Python for Programming. View other courses available at fredhutch.io
* fredhutch.io holds office hours Tuesdays from 9 am to noon (check CenterNet!), or ask Kate for individual appointments
* [The Coop](https://centernet.fredhutch.org/cn/u/bdsc.html): a centralized hub for data science at Fred Hutch
* [FHBig](https://fredhutch.github.io/FHBig/): community-focused events and Slack channel
* [Fred Hutch Biomedical Data Science Wiki](https://sciwiki.fredhutch.org): community-contributed resource for data management, bioinformatics, and computing
###### tags: `fredhutch.io` `python`