Bioinformatics and Genomics Tools

Tutorials:

Introduction to Bioinformatics and Computational Genomics for Stem Cell Biologists -  April 18th to April 21st, 2016

Workshop goals included:

  • Big picture of what bioinformatics and “-omics” analysis can do for you
  • Specific techniques in basic bioinformatics, genomics methods, databases
  • Basics of programming and data analysis in R
  • Best practices of documenting and sharing computational work
  • Use and contribute back to the PCBC C4 Omics data in Synapse
  • Perform end-to-end RNA-seq analysis
  • Hands on experience with data visualization, pathways and network analyses
  • ChiP-Seq peak calling and genomic variant analysis

Click on the link below to access session recordings:

https://www.synapse.org/#!Synapse:syn5885912


Using AltAnalyze to analyze Single Cell RNA-Seq (Part 1), May 9, 2015

Video illustrates how to analyze transcriptome datasets in AltAnalyze. Here we analyze a published single-cell gene expression dataset, supplied as a supplemental table, according to known biological groups and using a de novo group discovery workflow.

https://www.youtube.com/watch?v=npz34x0oILE

Using AltAnalyze to analyze Single Cell RNA-Seq (Part 2), May 9, 2015

Part 2 in a series of 3 Tutorials. Video illustrates how  to analyze transcriptome datasets in AltAnalyze. Here we analyze a published single-cell gene expression dataset, supplied as a supplemental table, according to known biological groups and using a de novo group discovery workflow.

https://www.youtube.com/watch?v=WySm7cQ13mw


Example of using the Expression Data explorer, March 8, 2015

This video demonstrates how to explore progenitor differentiation signatures quickly in Synapse (http://www.synapse.org) and ToppFun (https://toppgene.cchmc.org).

https://www.youtube.com/watch?v=eUOroAawY%5FE


WikiPathways

The PCBC Bioinformatics Core is posting a series of tutorials that will walk researchers through the process of creating reference digital pathways for analysis with their own omics data and those produced by the Cincinnati Cell Characterization Core (C4). It is recommended that people view these tutorials and follow along prior to group pathway creation or editing sessions.

Creating a WikiPathway using PathVisio, September 26, 2014

In this tutorial we walk you through the creation of a simple pathway, starting with selection of a pathway image, porting of the genes into the pathway, creating of objects and uploading to WikiPathways. For all objects in the pathway, comments and pubmed links can also be added as well as a description on the WikiPathway page.

http://youtu.be/GRtaLihkTGM

WikiPathways (WP) Flyers are attached below:
  • WikiPathways 1_Find Content
  • WikiPathways 2_Get Started
  • WikiPathways 3_Editing

Recorded Webinars:

Title: PCBC Introductory Genomics Webinar on  “Choosing the technology, designing the experiment, and preparing the samples to get the best data.”

Date: Friday, September 7, 2012

Presenter:  Dr. Mehdi Keddache

A recording is available for your review. Please click on the link below to play it:

https://epiumd.webex.com/epiumd/lsr.php?RCID=47c321c8fb8904305379ed63b5bd89d8


Title: Data Mining from the New Progenitor Cell Biology Consortium (PCBC) Genomics Expression Atlas

Date: Monday, July 29, 2013, 1:00 – 2:00 PM, EDT (12 Noon – 1:00 PM, CDT; 11:00 AM – 12 Noon, MDT; 10:00 AM – 11:00 AM, PDT)

Presenter: Bruce Aronow, Ph.D.

Topics for discussion:

  • Cell, RNA, and DNA samples in the PCBC Cell Characterization Core
  • Cell phenotype and genomics analyses have been performed (e.g., cell samples analyzed by RNAseq, miRseq, DNA methylation)
  • Finding what a gene of interest is doing in the different samples
  • Pathways and interactions that are active in different cells or involve genes of interest
  • Gene lists for similarity to signatures in the PCBC database
  • Splice forms of the RNAseq data from PCBC samples

Please click on the link below:

https://epiumd.webex.com/epiumd/lsr.php?RCID=330b9ad6a5986c13734b6a277970fb47 
 

Title: Bioinformatics Core - Synapse Webinar

Date/Time: Thursday, December 19, 2013, 1:00 pm – 2:00 pm (EST)

Presenters: Bruce Arnonow, Larsson Omberg, Nathan Salomonis

Click on the link below to play this webinar recording:

https://epiumd.webex.com/epiumd/lsr.php?RCID=3c06c71fae59d471433f7540bbeece4a


Title/Date: Accessing PCBC Generated Data in Synapse, June 5, 2014

Presenter: Larsson Omberg

The following topics were covered:

  • how to access, download, and query PCBC generated data as stored in Synapse,
  • how to use the PCBC web portal in Synapse to perform hierarchal clustering of user specified genes and link out to enrichment analysis,
  • how to get started in accessing the data from within R and Python, and
  • how to store your own analysis results in Synapse.

As the series progresses, more advanced topics in genomics and bioinformatics from visualization to batch correction to differential expression analysis will be covered.

Click on the link below to view the recording of this webinar:

https://www.youtube.com/playlist?list=PL0QrRbpf8KbSO8eTNFsIPUZJ85u6gtNkQ


Title/Date: Normalization, artifact detection and correction in Synapse, Friday, August 29, 2014

Presenter: Larsson Omberg

The second webinar covered the following topics:

* Principal component analysis and visualization

* Correlation analysis with covariates

* Corrections using Linear models

* Given enough time we will cover Surrogate Variable Analysis

 

Click on the link below to play this webinar recording:

http://youtu.be/ZcnSencVkEY


All these tutorial videos and webinars are also accessible in Synapse: https://www.synapse.org/#!Synapse:syn1773109/wiki/69076

 


Bioinformatics Course Materials in Synapse

2015 Bioinformatics course materials from the Stanford Stem Cell Course is available below:
https://www.synapse.org/#!Synapse:syn3270273

2014 Bioinformatics course materials from the Stanford Stem Cell Course is available below:
https://www.synapse.org/#!Synapse:syn2343177

 

 

 

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