Academy Documentation
  • Usage of Academy Documentation
  • Getting Started
    • Background Information
    • For Apollo Users
    • For Titan Users
    • For Scientists
    • For HPC Users
    • For Experienced Users
  • Cloud Computing
    • General Information
    • Cloud Computing for Scientists
    • Cloud Computing for HPC Users
  • Overview of the Platform
    • Overview of the Platform User Interface
    • Tool Library and App Introduction
  • Billing Access and Orgs
    • Orgs and Account Management
    • Billing and Pricing
  • Cohort Browser
    • Apollo Introduction
    • Overview of the Cohort Browser
    • Combining Cohorts
    • Genomic Variant Browser
    • Somatic Variants
  • JSON
    • Introduction
    • JSON on the Platform
  • Command Line Interface (CLI)
    • Introduction to CLI
    • Advanced CLI
  • Building Applets
    • Introduction
    • Bash
      • Example 1: Word Count (wc)
      • Example 2: fastq_quality_trimmer
      • Example 3: samtools
      • Example 4: cnvkit
      • Example 5: samtools with a Docker Image
    • Python
      • Example 1: Word Count (wc)
      • Example 2: fastq_quality_trimmer
      • Example 3: cnvkit
    • Publishing Applets to Apps
  • Building Workflows
    • Native Workflows
    • WDL
      • Example 1: hello
      • Example 2: Word Count (wc)
      • Example 3: fastq_trimmer
      • Example 4: cnvkit
      • Example 5: workflow
    • Nextflow
      • Resources To Learn Nextflow
      • Overview of Nextflow
      • Nextflow Setup
      • Importing Nf-Core
      • Building Nextflow Applets
      • Error Strategies for Nextflow
      • Job Failures
      • Useful Information
  • Interactive Cloud Computing
    • Cloud Workstation
    • TTYD
    • TTYD vs Cloud Workstation
    • JupyterLab
      • Introduction
      • Running a JupyterLab Notebook
  • Docker
    • Using Docker
    • Creating Docker Snapshots
    • Running Docker with Swiss Army Knife
  • Portals
    • Overview of JSON files for Portals
    • Branding JSON File
    • Home JSON File
    • Navigation JSON File
    • Updating Your Portal
  • AI/ ML Accelerator
    • Data Profiler
      • Introduction to Data Profiler
      • Utilizing Data Profiler Navigator
      • Dataset Level Screen
      • Table Level Screen
      • Column Level Screen
      • Explorer Mode
      • Accessing Data Profiler in ML JupyterLab
    • ML JupyterLab
      • Introduction to ML JupyterLab
      • Launching a ML JupyterLab Job
      • In App Features
      • Getting Started with ML JupyterLab
    • MLflow
      • Introduction to MLflow
      • Getting Started with MLflow
      • Using MLflow Tracking Server
      • Model Registry
      • Using Existing Model
      • Utilizing MLflow in JupyterLab
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  • Programming Languages
  • Reproducible Research
  • Biology Concepts

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  1. Getting Started

Background Information

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Last updated 1 year ago

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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

Python

R

Reproducible Research

Biology Concepts

Ten Simple Rules for Getting Started with Command-Line Bioinformatics
The Unix Shell
Unix Command Cheatsheet
Bash for Bioinformatics
Programming with Python
Plotting and Programming in Python
Learn Python
Ten Simple Rules for Teaching Yourself R
Programming with R
R for Reproducible Scientific Analysis
Swirl for R
The Five Pillars of Computational Reproducibility: Bioinformatics and Beyond
Version Control with Git
Cancer Biology Medicine: Next Generation Sequencing and its Clinical Application
A Beginner's Guide to Analysis of RNA Sequencing Data