myExperiment - Workflows

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Tag: snp

User: Pierre Lindenbaum

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XProc

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Pierre Lindenbaum

Query dbsnp, transform to HTML (1)

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This is a XProc worklow. Its input is a list of Entrez queries packed in a html list: See http://plindenbaum.blogspot.com/2009/05/xml-pipelines-xproc-for-bioinformatics.html "snp_gene_clin"[Filter] AND "snp_pubmed_cited"[Filter] AND 2[CHR] (1000[CHRPOS] : 5000[CHRPOS]) AND 2[CHR] AND "homo sapiens"[Organism] it queries entrez, download the SNPs as XML and transform the result as an HTML table: r...

Created: 2009-05-21 | Last updated: 2009-05-21

Credits: Pierre Lindenbaum

Taverna 1

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Pierre Lindenbaum

snpNeighbours (1)

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My first Taverna workflow: the input is the SNP "rs25". The Web Services invoked finds its position on the human genome and find its neighbours at 100bp. The XML result is then saved to a local file. The web services used here are under developpement and might be turned off in a near future.

Created: 2009-05-14 | Last updated: 2009-05-14

Credits: Pierre Lindenbaum

KNIME

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Pierre Lindenbaum

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: Pierre Lindenbaum

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