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HPCBIO WORKSHOPS

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UPCOMING WORKSHOPS

Microbiome rRNA amplicon analysis

This workshop will be offered on four consecutive Fridays starting September 29th, 2017. For more details and sign-up information click here: https://www.eventbrite.com/e/microbiome-rrna-amplicon-analysis-registration-36660706159.

Additional News

In the near future we hope to offer workshops covering Linux and R Basics, and CHIP-Seq analysis. 

We would love your input as to what kind of topics you'd like to see covered in an HPCBio workshop for the future, so please let us know in this 2 question survey: https://goo.gl/forms/OHxrQwiTDqrZsHmh2.


 

PREVIOUS WORKSHOP MATERIALS
 
Creative Commons License
HPCBio Workshop materials are licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
 
 
QIIME for microbiome analysis (+ Intro to Linux)

Description: QIIME is an open-source pipeline for preprocessing and analyzing raw rRNA amplicon sequences for microbiome analysis. This allows researchers to not only investigate what organisms are present in their microbiome of interest, but also to calculate and visualize diversity using common diversity metrics. This workshop first aims to familiarize attendees with basic Linux commands necessary to run QIIME and to give an introduction to amplicon design and sequencing. Attendees will then learn how to perform upstream (preprocessing, OTU picking, alignment & tree building) and downstream analyses (alpha & beta diversity, visualizations, & statistics).

Link to Materials:

July 2016

August 2015

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Introduction to R

Description: R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data, including Next Generation Sequencing (NGS) data. This workshop aims to take the novice and turn them into a beginning R user. We will describe the R environment and programming language structure so that students can start to read and write code and know where to get additional help.

Links to Materials:

Fall 2016

Fall 2015

Spring 2015

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Introduction to R and Bioconductor

Description: R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data, including Next Generation Sequencing (NGS) data. This workshop aims to take the novice and turn them into a beginning R/Bioconductor user. We will describe the R environment and programming language structure so that students can start to read and write code and know where to get help. Additonally, we will give an overview of the Bioconductor project, common object structures and manipulation, tips on finding particular packages and how to start learning to use a package.

Links to Materials:

Spring 2016

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Introduction to Linux and Biocluster

Description: The Linux command line interface is a text-based way of interacting with a computer, particularly high performance computer systems that are capable of analyzing NGS data. The most common and cutting-edge bioinformatics tools are best run via the command line. This is a workshop for biologists who want to get acquainted with using the Linux command line interface. Additionally, the workshop will cover the basics of cluster computing and how to navigate and submit jobs to IGB’s Biocluster high performance computing environment.

Links to Materials:

Fall 2016

Spring 2016

Fall 2015 

Spring 2015

Fall 2014

 
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RNA-Seq analysis with Biocluster and R

Prerequisite: R, Linux, & Biocluster knowledge

Description: Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it can be done on any species.  This is a 4-day workshop for biologists who are doing or plan on doing RNA-Seq experiments and would like to learn how to analyze their data. It will cover experimental design, evaluation of sequencing quality, genome alignment, gene count extraction, differential gene expression analysis and downstream data mining. It will also include discussions of what to do if your species lacks gene models and/or a genome.

Links to Materials:

Spring 2017

Fall 2016

Spring 2016

Fall 2015 

Spring 2015

 
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Description: This workshop is geared towards biologists who would like to learn the tools for graphical representation and visualization of genomics data. The focus will be on two genome browsers, Integrative Genomics Viewer (IGV) and the Ensembl browser, and Ensembl's BioMartThis workshop will cover how to use each browser, including the use of pre-generated datasets and custom datasets.

Link to Materials:

Spring 2016

Spring 2014 

 

Computational Skills for Genomics Workshop

Description: This hands-on workshop, jointly taught by HPCBio and CNRG, aims to introduce you to high performance cluster computing, linux command line, R programming and Bioconductor packages. In addition, attendees will learn how to move data to a computational cluster, and perform initial quality control steps on sequence reads using FASTQC. Knowledge of Linux and R can be very useful for analyzing genomics and many other -omics data. At the end of this workshop you will gain a familiarity with Linux and R commands. You will not become an expert in genomics analysis techniques, but you will get an idea of where to start when given raw sequence data.

Link to Materials:

March 2017

 

Data Carpentry Genomics Workshop

Description: Join this workshop being conducted by HPCBio, CSE, and KnowEng to learn basic skills necessary to get you started working on genomic data. This includes hands-on introductions to high performance cluster computing, linux command line, best data tidiness practices, R programming and Bioconductor packages. In addition, attendees will learn how to move sequencing data to a computational cluster, and perform initial quality control steps.

Link to Materials:

Summer 2016

Summer 2015