An Overview of GenePattern 3.8.0

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This video covers some of the new features of GenePattern 3.8.0, including:

* Pinning modules
* Adding pipelines to multiple categories
* Dynamically populated dropdown menus for modules
* File purge based on users & groups
  1. GenePattern
  2. GenePattern
  3. Broad Institute
  4. Software
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Gene expression analysis using the ComparativeMarkerSelection tool in GenePattern

Extracting a list 0:01:30

Extracting a list of genes using the ExtractComparativeMarkerResults tool in GenePattern

Converting Expression Data 0:04:26

Converting Expression Data into a GenePattern input file format

Evaluate the differential 0:02:30

Evaluate the differential expression of a dataset using Cufflinks.cuffdiff in GenePattern

RNA-seq QC in 0:09:48

RNA-seq QC in GenePattern

Aligning RNA-Seq reads 0:02:29

Aligning RNA-Seq reads to a reference genome using TopHat in GenePattern

Perform Gene Set 0:00:59

Perform Gene Set Enrichment Analysis

Identifying differential gene 0:01:19

Identifying differential gene expression in RNA-seq reads

HOW TO PERFORM 0:48:10

HOW TO PERFORM GSEA - A tutorial on gene set enrichment analysis for RNA-seq

Identify biological functions 0:05:28

Identify biological functions for genes in CNV regions using GenomeSpace

Driving Biological Project 0:04:18

Driving Biological Project - Step 1

Importing data to 0:00:38

Importing data to Galaxy

Driving Biological Project 0:09:10

Driving Biological Project - Step 3

Download a collection 0:00:41

Download a collection of chromosome cytoband gene sets

Gene Set Enrichment 0:10:01

Gene Set Enrichment Analysis: Human Gage on T BioInfo

Transfer the RNA-seq 0:00:59

Transfer the RNA-seq and MAF data files from GenomeSpace to Galaxy

Normalize breast cancer 0:00:55

Normalize breast cancer copy number variation profiles

Converting BAM to 0:00:55

Converting BAM to BigWig

Gencodr: Gene Set 0:10:07

Gencodr: Gene Set Enrichment Analysis with Deep Learning

Driving Biological Project 0:01:08

Driving Biological Project - Step 8

Driving Biological Project 0:02:40

Driving Biological Project - Step 5

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Driving Biological Project 0:06:22

Driving Biological Project - Step 9

Gene Expression Matrices 0:06:59

Gene Expression Matrices