All content

Microarray CEL file to candidate pathways (2)

This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) http://www.bioinf.manchester.ac.uk/MADAT/index.html. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ch...

Created: 2008-02-08 | Last updated: 2009-02-13

Credits: Paul Fisher Saeedeh

AffyArrayNormalization (2)

• Download

The AffyArrayNormalization web services normalise raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's normalization R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayNormalization services. The flow is as follows: A client executes the AffyArrayNormalization_submit service with two inputs: a User object and a collection of URLs linking to CEL files. The User object contains a user ID, a password and an ...

Created: 2009-02-16 | Last updated: 2009-02-16

Credits: Pieter Neerincx Philipg

AffyArrayQualityAnalysis (2)

• Download

The AffyArrayQualityAnalysis web services provide quality control for raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's quality control R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayQualityAnalysis services. The flow is as follows: A client executes the AffyArrayQualityAnalysis_submit service with two inputs: a User object and a collection of URLs linking to CEL files. The User object contains a u...

Created: 2008-03-13 | Last updated: 2009-02-16

Credits: Pieter Neerincx Philipg

Human Microarray Analysis (1)

This workflow takes in probesets from and AffyMetrix  Affy HG U133A micorarray experiment and returns: genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data.   Example input for this workflow is: 212283_at 221634_at 220399_at  

Created: 2008-02-08 | Last updated: 2009-12-03

Credits: Paul Fisher

Load affymetrix experiments results into S... (1)

• Download

The affymetrix data source is not public.

Created: 2009-02-17

Credits: Francois Belleau

Initialize triplestore with Murin's protoc... (1)

• Download

This workflow initialize the Sesame triplestore with initial data.  The 5 rdfiser in JSP are needed, they are executed on localhost.

Created: 2009-02-17 | Last updated: 2009-02-17

Credits: Francois Belleau

Gene set enrichment analysis (Affymetrix p... (1)

• Download

This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at http://www.broadinstitute.org/gsea/index.jsp. As input, the normalized data with Affymetrix probeset IDs can be submitted.First, the input files are subjected to fold-change calculation. The table with probeset Ids and calculated fold change values is converted into a table with Ensembl Gene Ids. At the next step, the Ensembl genes are annotated with additional information, gene description and gene...

Created: 2013-10-29 | Last updated: 2015-04-17

Credits: geneXplain

View Download

Ensembl gene report

Created: 2009-04-08 19:30:15 | Last updated: 2009-08-10 11:05:59

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

Comments: 0 | Viewed: 91 times | Downloaded: 58 times

View Download

Tir1 QTL - microarray day 7 intersecting pathways

Created: 2009-04-08 17:57:57

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

Comments: 0 | Viewed: 89 times | Downloaded: 68 times

View Download

Candidate Gene protocol

Created: 2009-04-08 13:27:20

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word document

Comments: 0 | Viewed: 122 times | Downloaded: 85 times