> For the complete documentation index, see [llms.txt](https://academy.dnanexus.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://academy.dnanexus.com/getting-started/docs_programming.md).

# Background Information

Welcome to DNAnexus!

Before you go through the information here, there is necessary information that we think will be useful for you to have.

Some of the users of the platform have limited coding experience. As bioinformaticians and computational biologists, we are members of a community that want to help alleviate that stress. On this page, we attached some helpful links and tutorials that will hopefully help make the world of computational biology a bit less intimidating. This is not a partnership or affiliation, but rather a list of what we found useful when we were learning ourselves.

Additionally, users may need resources on the different types of sequencing and the impacts, and we have some here for the ever evolving field of genetics/ genomics. Again, these are not endorsing any particular company, lab, or resource, but instead more of a general guide to help fill in the gaps.

### Programming Languages

#### Bash

* [Ten Simple Rules for Getting Started with Command-Line Bioinformatics](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008645)
* [The Unix Shell](https://swcarpentry.github.io/shell-novice/)
* [Unix Command Cheatsheet](https://commons.wikimedia.org/wiki/File:Unix_command_cheatsheet.pdf)
* [Bash for Bioinformatics](https://laderast.github.io/bash_for_bioinformatics/06-JSON.html)

#### Python

* [Programming with Python](https://swcarpentry.github.io/python-novice-inflammation/)
* [Plotting and Programming in Python](https://swcarpentry.github.io/python-novice-gapminder/)
* [Learn Python](https://www.learnpython.org/)

#### R

* [Ten Simple Rules for Teaching Yourself R](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010372)
* [Programming with R](https://swcarpentry.github.io/r-novice-inflammation/)
* [R for Reproducible Scientific Analysis](https://swcarpentry.github.io/r-novice-gapminder/)
* [Swirl for R](https://swirlstats.com/students.html)

## Reproducible Research

* [The Five Pillars of Computational Reproducibility: Bioinformatics and Beyond](https://academic.oup.com/bib/article/24/6/bbad375/7326135)
* [Version Control with Git](https://swcarpentry.github.io/git-novice/)

## Biology Concepts

* [Cancer Biology Medicine: Next Generation Sequencing and its Clinical Application](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6528456/#:~:text=Next%2Dgeneration%20sequencing%20\(NGS\),a%20short%20period%20of%20time.)
* [A Beginner's Guide to Analysis of RNA Sequencing Data](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096346/)