Create a module in GenePattern

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This demonstration shows how to create your own custom analysis module in GenePattern using the module integrator to wrap a script or command line utility.
  1. GenePattern
  2. GenePattern
  3. Broad Institute
  4. bioinformatics
  5. programming languages
  6. reproducible research
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Create a module 0:05:43

Create a module in GenePattern

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Creating a pipeline of modules for analyzing RNA-Seq data in GenePattern

Running a pipeline 0:02:29

Running a pipeline of modules for analyzing RNA-Seq data in GenePattern

Creating a module 0:01:34

Creating a module network using Genomica

Submitting your module 0:03:32

Submitting your module to GParc

An Overview of 0:04:43

An Overview of GenePattern 3.8.0

Sending data from 0:00:44

Sending data from GenomeSpace to GenePattern's PreprocessDataset module

Using GenePattern Protocols 0:04:17

Using GenePattern Protocols

Trimming files in 0:00:53

Trimming files in GenePattern using the SelectFileMatrix module

Exploring the New 0:05:55

Exploring the New GenePattern Pipeline Designer

Converting Ilumina Expression 0:04:18

Converting Ilumina Expression Data Into the GenePattern GCT format

Importing Data from 0:03:51

Importing Data from caArray to GenePattern

Export Datasets from 0:04:21

Export Datasets from InSilicoDB to GenePattern

Finding differentially expressed 0:00:49

Finding differentially expressed genes (GenePattern 'ComparativeMarkerSelection' Module)

Gene expression analysis 0:01:07

Gene expression analysis using the ComparativeMarkerSelection tool in GenePattern

Batch Execution in 0:04:18

Batch Execution in GenePattern 3.3.3

Processing the reference 0:01:14

Processing the reference genome using Picard.CreateSequenceDictionary and SAMtools.FastaIndex

GenePattern: Getting Started 0:05:15

GenePattern: Getting Started

GenePattern Notebook 2020 0:03:01

GenePattern Notebook 2020 Update

Differential Expression Analysis 0:07:25

Differential Expression Analysis with RNA-seq data using GenomeSpace

Converting Between MAGE-TAB 0:07:15

Converting Between MAGE-TAB and GenePattern Expression File Formats

Extracting a list 0:01:30

Extracting a list of genes using the ExtractComparativeMarkerResults tool in GenePattern

Using the GenePattern 0:04:04

Using the GenePattern Uploads Tab

Create an index 0:02:27

Create an index for a BAM file using the Picard.SortSam tool in GenePattern