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fixing/adding/changing links #1

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fixing/changing/adding links
e-hutchins Dec 18, 2018
41cedad
Merge pull request #1 from e-hutchins/e-hutchins-patch-1
e-hutchins Dec 18, 2018
21de792
overall updates, adding R Shiny and MySQL
e-hutchins May 18, 2020
f4b796f
add link to maintained repo
e-hutchins May 20, 2020
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37 changes: 34 additions & 3 deletions README.md
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This parent repo is no longer maintained. The fork currently being maintained is here:
https://github.com/e-hutchins/BioinformaticsIntroduction


# Bioinformatics Introduction

Here we compile our best practices for introducing new trainees to computational biology.
Expand Down Expand Up @@ -41,10 +45,13 @@ Alternatively you may want a GUI-based text editor, like Sublime:

https://www.sublimetext.com/

Or Atom:
https://atom.io/

## 3. Introduction to python
There are many different languages that we can write code or scripts in for analyzing our data. One of the most commonly used langauges in bioinfomatics is python. The tutorial at codecademy can help you get started with learning python syntax, though there are many other places to learn coding in python.

https://www.codecademy.com/learn/python
https://www.codecademy.com/learn/learn-python-3

For advanced python, you can run through the Python Data Science Handbook:

Expand All @@ -65,6 +72,10 @@ Similar to python, there are many tutorials for R, but one that many trainees in

https://www.datacamp.com/courses/free-introduction-to-r

Alternatively, Data Carpentry has in Intro to R course:

http://datacarpentry.org/R-ecology-lesson/index.html

Here are videos for how to do basic computation in R, and basic programming in R:

https://www.youtube.com/watch?v=3xriAzqc-fw
Expand All @@ -73,6 +84,10 @@ Here are videos for how to do basic computation in R, and basic programming in R
For advanced R practice, you can run through R for Data Science:

http://r4ds.had.co.nz

R for Data Science solutions are available here:

https://jrnold.github.io/r4ds-exercise-solutions/

Or you can work in R studio using the swirl R package:

Expand Down Expand Up @@ -133,16 +148,32 @@ Common SFTP GUIs are CyberDuck:
https://cyberduck.io/
And FileZilla:

https://cyberduck.io/
https://filezilla-project.org/

## 9. Snakemake
One of the first rules of bioinformatics is that it is (nearly) always worth the time to make your analysis reproducible. Snakemake can help you with reproducible analyses.

You can start out with this video:

https://youtu.be/naRvlRpXLe8
https://youtu.be/8xnm_RKkycQ

And this tutorial:

http://slowkow.com/notes/snakemake-tutorial/


## 10. R Shiny
It can be useful to create interactive plots for your data. One way to do this is with R Shiny.

https://shiny.rstudio.com/tutorial/

## 11. Databases - MySQL
Sometimes you may want to create or interact with databases in R.

Here is an introduction in creating MySQL databases and querying them with R:

https://programminghistorian.org/en/lessons/getting-started-with-mysql-using-r

And some information on R Shiny database basics:

https://shiny.rstudio.com/articles/overview.html