GCD Bioinformatics Resources

Welcome to the GCD bioinformatics resources page.

I will be using this space to share resources and information with the department.  I will also be highlighting some of the projects I have worked to give a sense of what kind of projects I have worked on and how these bioinformatics tools might be able to help your research.  Please feel free to send me requests for tutorials or ask questions that might be of general interest.


Micah Gearhart, PhD

gearh006@umn.edu
@micahgearhart

Location:
5-147 Moos Tower
515 Delaware St SE
Minneapolis, MN 55455

Campus Mail:
6-160 Jackson Hall
321 Church St
Minneapolis, MN 55455


Tutorials (Coming soon):
Genomics Data Visualization 101
How to Find and Utilized NGS Data in Public Repositories
RNA-Seq Data Analysis with DESeq2

HarvardX is offering an online bioinformatics course for RNA-Seq / Microarray Data that will feature DNASeq2.  It's free and starts April 7th.

FAQ (Coming Soon):
Galaxy, CLC Genomics, or Command line – what is right for me?
I just got my RNA-Seq dataset, now what?

Recommended Software:
Here are some links to recommended software resources.  I have varying amounts of familiarity with resources – some I have used once or twice, some once or twice a day.   If there is something that is not on this list that you would like some help with,  let me know and I can maybe help you get up and running.

Genome Mapping and Processing:
   BWA
   Bowtie
   FASTQC
   Picard
   Samtools

Transcriptome Mapping:
  Star
  Tophat

Micrarray Analysis:
   Limma /Geo2R

RNA-Seq Differential Expression:
  EdgeR
  DESeq2

ChIP-Seq Peak Detection
  MACS

Variant Detection  
  GATK

Annotation
  DAVID
  Ingenuity / IPA
  AnnotationHub
  Biomart