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Showing 9 results. Use the filters on the left and the search box below to refine the results.
Tag: ngs Licence: by-sa

Workflow RNA-Seq workflow with TopHat and Cufflinks... (1)

An example workflow demonstrating the RNA-seq analysis using Bioextract Server. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. (Ref: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html).

Created: 2013-11-09 | Last updated: 2014-04-10

Credits: User zohim User Carol Lushbough User Bioextract Network-member BioExtract Server for Genomics

Workflow Compute and correct GC bias in NGS data (1)

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Galaxy workflow based on deepTools which will compute and correct GC bias in your NGS data. For more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03

Credits: User Björn Grüning

Workflow Heatmap of read coverages (single BAM file) (1)

Galaxy workflow based on deepTools which creates a clustered heatmap of the read coverage. One BAM file will be used as input and a heatmap will be the output.For more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03

Credits: User Björn Grüning

Workflow Heatmap of read coverages (1)

Galaxy workflow based on deepTools which creates a clustered heatmap of the read coverage. Two BAM files will be used as input and a heatmap will be the output.For more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03

Credits: User Björn Grüning

Workflow Clustered heatmap of signals around the TSSs (1)

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Galaxy workflow based on deepTools which creates a clustered heatmap of signals around the TSS. One bigwig file is needed as input with the signal and an annotation file with your TSS regions. The output will be a heatmap. You can create such a bigwig file with the bamCorrelate toolFor more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03 | Last updated: 2014-04-03

Credits: User Björn Grüning

Workflow Running a picard tool in the #KNIME workfl... (1)

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Running a picard tool in the #KNIME workflow engine . See my blog http://plindenbaum.blogspot.fr/2013/07/running-picard-tool-in-knime-workflow.html

Created: 2013-07-18

Credits: User Pierre Lindenbaum

Blob Getting Started with Taverna - an NGS tutorial

Created: 2012-05-23 14:53:24 | Last updated: 2012-05-30 08:48:19

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial is an introduction to using Taverna, using an example from Chip-Seq analysis

File type: PowerPoint presentation

Comments: 0 | Viewed: 72 times | Downloaded: 80 times

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Workflow Define Associated Regions and Genes (2)

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Defines regions and genes from associated SNPs A JAVA MySQL connector is required to run the workflow and must be placed in the $TAVERNA_HOME/lib directory.

Created: 2012-02-08 | Last updated: 2012-05-09

Credits: User Paul martin

Workflow The NOTCH2 workflow (1)

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Analysis of the exome sequencing data for the following article: Nat Genet. 2011 Mar 6;43(4):306-8. Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis. Isidor B, Lindenbaum P, Pichon O, Bézieau S, Dina C, Jacquemont S, Martin-Coignard D, Thauvin-Robinet C, Le Merrer M, Mandel JL, David A, Faivre L, Cormier-Daire V, Redon R, Le Caignec C. using knime4bio

Created: 2011-09-06 | Last updated: 2011-09-06

Credits: User Pierre Lindenbaum

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