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Items tagged with "microarray" (14)

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Pack Microarray data analysis using R

Created: 02/07/08 @ 11:30:06 | Updated: 02/07/08 @ 11:30:06

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Blob A Taverna Users Guide

Created: 04/08/08 @ 17:40:21 | Updated: 04/08/08 @ 17:40:21

Credits: User Paul Fisher User Katy Wolstencroft User Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 License

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Workflows (12)

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Workflow HUMAN Microarray CEL file to candidate pathways (v4)

Created: 03/10/07 @ 18:35:55 | Updated: 04/04/08 @ 12:14:20

License: Creative Commons Attribution-NoDerivs 3.0 License

Microarray_cel_file_to_candidate_pathways_17032_4
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 ...

Rating: 5.0 / 5 (1 rating) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow KEGG pathways common to both QTL and microarray based investigations (v2)

Created: 03/10/07 @ 18:35:58 | Updated: 13/11/07 @ 16:22:14

License: Creative Commons Attribution-NoDerivs 3.0 License

Kegg_pathways_common_to_both_qtl_and_microarray_based_investigations_27627
This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 1

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Workflow Query Maxd microarray database (v1)

Created: 14/11/07 @ 16:01:50 | Updated: 22/11/07 @ 12:06:32

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 License

Query_maxd_microarray_database_5480
Retrieves data from the maxd database given name of data set

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Workflow Mapping microarray data onto metabolic pathways (v1)

Created: 14/11/07 @ 16:51:26 | Updated: 22/11/07 @ 10:39:32

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 License

Mapping_microarray_data_onto_metabolic_pathways_3766
This workflow maps microarray data onto metabolic pathway diagrams represented as SBML models drawn using Cell Designer. To run this workflow requires libsbml to be installed into taverna - see http://www.mcisb.org/software/taverna/libsbml/index.html

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Workflow Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Updated: 14/05/08 @ 15:43:16

Credits: User Paul Fisher User Saeedeh

License: Creative Commons Attribution-Share Alike 3.0 License

Microarray_cel_file_to_candidate_pathways_1844_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 ...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Human Pathways from Diff Expressed Genes (v1)

Created: 08/02/08 @ 14:30:17 | Updated: 08/02/08 @ 14:30:17

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

Human_pathways_from_diff_expressed_genes_4391_1
This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data

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Workflow AffyArrayQualityAnalysis (v2)

Created: 13/03/08 @ 14:38:03 | Updated: 13/03/08 @ 14:40:37

Credits: User Pieter Neerincx User Philipg

License: Creative Commons Attribution-Share Alike 3.0 License

Affyarrayqualityanalysis_27323_2
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 to CEL files. * The User object contains a user ID, a passw...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow AffyArrayNormalization (v1)

Created: 13/03/08 @ 14:47:39 | Updated: 13/03/08 @ 14:47:39

Credits: User Pieter Neerincx User Philipg

License: Creative Commons Attribution-Share Alike 3.0 License

Affyarraynormalization_76_1
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 to CEL files. * The User object contains a user ID, a password and an e-mail address....

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Workflow Identification of differential genes using t-tests by R (v2)

Created: 15/04/08 @ 15:37:42 | Updated: 01/07/08 @ 17:21:18

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 License

Identification_of_differential_genes_using_t-tests_by_r_3052_2
This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data for analysis using t-tests by R. A list of significant differentially expressed genes is then analysed using the Go Term Finder tool which generates a list of GO terms associated with the genes. A CSV file containing the list of significant genes is also generated.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Identification of differential genes using the LIMMA Bioconductor package within R (v1)

Created: 02/07/08 @ 11:24:12 | Updated: 02/07/08 @ 11:28:21

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 License

Identification_of_differential_genes_using_t-tests_by_r_1181_1
This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data which are then analysed by the LIMMA Bioconductor package in an R script. This produces a list of significant differentially expressed genes which is then analysed using the Go Term Finder tool to generate a PDF report of the common GO terms associated with the genes. A CSV file containing the list of sign...

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Workflow Pathways from Diff Expressed Genes (v3)

Created: 03/10/07 @ 18:36:05 | Updated: 11/07/08 @ 10:52:01

License: Creative Commons Attribution-Share Alike 3.0 License

Pathways_from_diff_expressed_genes_22895_3
This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2.

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 1

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Workflow Pathways from Diff Expressed Genes (v3)

Created: 03/10/07 @ 18:36:05 | Updated: 11/07/08 @ 10:52:01

License: Creative Commons Attribution-Share Alike 3.0 License

Pathways_from_diff_expressed_genes_22895_3
This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2.

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 1

Viewed: 874 times | Downloaded: 799 times

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