01:20

Call and filter variants with FreeBayes and the VCFlib toolkit

01:06

Loading Data into Galaxy

01:21

Visualize variants

00:41

Download a collection of chromosome cytoband gene sets

00:55

Normalize breast cancer copy number variation profiles

01:46

Sort breast cancer tumor samples based on the presence or absence of the stemness signature

01:52

Compare copy number variation data to identify regulators of expression

01:36

Obtain a list of candidate stemness regulators

00:27

Convert the processed RNA-seq file into a GCT file

02:05

Obtain input files from FireBrowse

04:10

Create a CLS file using the list of ERCC2-mutated samples

01:24

Upload and un-zip FireBrowse data in GenomeSpace

00:59

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

01:02

Process the RNA-seq file in Galaxy

01:53

Reprocess the filtered RNA-seq data into a new file

01:52

Identify RNA-seq samples that have MAF annotations by overlapping files

00:49

Extract regions of significantly different genes

01:03

Importing Galaxy workflow to identify regions of significantly different genes

00:38

Importing data to Galaxy

00:55

Converting BAM to BigWig

00:41

Converting peak files to BigWig for visualization in IGV

01:03

Identifying peak-enriched regions from ChIP-seq data

01:23

Identifying DNA modification regions and their influence on associated gene expression

03:38

Visualization in IGV

00:54

Sending data to GenomeSpace for visualization in IGV

01:19

Identifying differential gene expression in RNA-seq reads

00:50

Obtaining a reference genome using Galaxy

00:50

Running gene set analysis in Genomica

00:59

Perform Gene Set Enrichment Analysis

01:15

Finding genes in CNV regions

00:54

Identifying highly connected subnetworks using the MCODE module in Cytoscape 3

01:41

Building a network from a gene list using the GeneMANIA module in Cytoscape 3

01:21

Loading data into Cytoscape 3 from GenomeSpace

01:28

Filter a network of nodes and edges in Cytoscape3

01:08

Visualizing and Filtering a Gene Regulatory Network in Cytoscape3

29:10

GenomeSpace Orientation Webinar - October 24, 2016

39:45

GenomeSpace Recipe Webinar - June 27, 2016 - Find Differentially Expressed Genes in RNA-Seq Data

01:16

Filter and convert read counts to logCPM

01:33

Remove batch effects using ComBat

02:03

Importing and running a Galaxy workflow v2

01:42

Principal Component Analysis of an expression dataset

02:29

Visualizing a Principal Component Analysis

23:24

GenomeSpace Orientation Webinar - Feb. 29, 2016 - Question & Answer session

35:58

GenomeSpace Orientation Webinar - Feb. 29, 2016 - Webinar Presentation

03:19

Visualizing coding variants in IGV

02:10

Importing and running a Galaxy workflow

00:53

Transferring files from Galaxy to GenomeSpace

01:19

Search for significant overlap with known genesets using MSigDB

00:51

Trimming files using the "Text Manipulation" tool in Galaxy

00:44

Find genes in CNV regions using the "Operate on Genomic Intervals" tool in Galaxy

01:30

Loading data into Galaxy from GenomeSpace

01:30

Extracting a list of genes using the ExtractComparativeMarkerResults tool in GenePattern

00:41

Identifying highly connected subnetworks using the MCODE module in Cytoscape 2

00:57

Obtaining a reference genome from the UCSC Table Browser (BED files)

01:07

Gene expression analysis using the ComparativeMarkerSelection tool in GenePattern

01:13

Loading data into Cytoscape 2 from GenomeSpace

01:36

Viewing results of gene expression analysis using ComparativeMarkerSelectionViewer in GenePattern

00:41

Identifying duplicate reads in RNA-Seq data using Picard.MarkDuplicates in GenePattern

01:44

Reannotating an RNA-Seq dataset using Picard.ReorderSAM and Picard.AddOrReplaceReadGroups

01:41

Building a network from a gene list using the GeneMANIA module in Cytoscape 2