Workflows

Variant Annotation with VEP (Variant Effec... (1)

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Here, from a list of g.vcf files, we execute GenotypeGVCFs command line GenotypeGVCFs perform joint genotyping on gVCF files produced by HaplotypeCaller Variant Effect Predictor http://www.ensembl.org/info/docs/tools/vep/script/index.html The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Created: 2016-05-16 | Last updated: 2016-07-06

Metavisitor: Workflow for Use Case 3-2 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-05-13 | Last updated: 2017-04-17

Metavisitor: Workflow for Use Case 3-1 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-05-13 | Last updated: 2017-04-17

Metavisitor: Workflow for Use Case 2-2 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedoc Mississippi Galaxy server 

Created: 2016-05-13 | Last updated: 2017-04-17

Metavisitor: Workflow for Use Case 2-1 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-05-13 | Last updated: 2017-04-17

Metavisitor: Workflow for Use Case 1-2 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server

Created: 2016-05-13 | Last updated: 2017-04-17

Metavisitor: Workflow for Use Case 1-1 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-05-13 | Last updated: 2017-04-17

Data Mining Recommender (4)

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Scientific workflow for the recommender construction 

Created: 2014-10-29 | Last updated: 2018-09-20

Credits: respinosa

MsaPAD: Multiple Sequence Alignment - Inpu... (2)

BioVeL – Biodiversity Virtual e-Laboratory Workflow Documentation Name:Perform a Multiple DNA sequence alignment coding for multiple/single protein domains Capacities Programme of Framework 7: EC e-Infrastructure Programme – e-Science Environments - INFRA-2011-1.2.1 Grant Agreement No: 283359 Project Co-ordinator: Mr Alex Hardisty Project Homepage: [http://www.biovel.eu][1] [1]: http://www.biovel.eu ## 1 Description This workflow is used to submit the multip...

Created: 2014-07-30 | Last updated: 2015-06-12

Credits: Bachirb Giacinto Donvito Pasquale Notarangelo Saverio Vicario Graziano Pesole

Attributions:

Imagemagick convert - tiff/png/bmp/jpeg2ti... (2)

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Converts tiff to tiff/png/bmp/jpeg using imagemagick convert with the provided compression

Created: 2014-02-14 | Last updated: 2014-11-06

Credits: Markus Plangg

MrBayes (10)

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using slow paced JSTasync 1

Created: 2013-12-11 | Last updated: 2014-06-19

JSTAsync1 (6)

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slow down job retrival to one every 60 sec

Created: 2013-12-11 | Last updated: 2014-06-19

JSTAsync2 (7)

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slow down loops to 60 sec

Created: 2013-12-11 | Last updated: 2014-06-19

Annotate gene list with top ranking concepts (4)

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This workflow annotates a comma separated gene list with a predefined concept set as for example Biological processes or Disease/syndrome. To obtain the particular id for each concept set (e.g. "5" for Biological processes), the workflow listPredefinedConceptSets needs to run first. The output provides us with the top (cutoff) concepts that describe our gene list of interest The workflow is using the anni web services .

Created: 2013-12-03 | Last updated: 2015-04-03

Credits: Eleni

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

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

Credits: zohim Carol Lushbough Bioextract BioExtract Server for Genomics

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

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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

Metabolic differences in ripening of Solan... (2)

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Updated data processing workflow for metabolomics LC-MS/MS data. This workflow depends on the stable community plug-in MassCascade and KNIME plug-ins Base Chemistry, Chemistry Types & Nodes, Math Expression, and XLS Support. The workflow was run under KNIME version 2.9.2.

Created: 2013-10-16 | Last updated: 2014-07-04

Credits: SBeisken

Clustering of Molecular Compounds with Bio... (4)

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This workflow downloads an input set of molecular compounds in SMILES format, using Chemspider service. The most frequent molecular fragments are extracted by means of MoSS tool (see http://www.borgelt.net/moss.html) , in order to obtain a set of features for each compound. Then a clustering and a visual exploration of the input dataset is performed by BioDICE service (see http://biolab.pa.icar.cnr.it/biodice.html), implementing Fast Learning Self-Organized Map (FLSOM) algorithm. Finally the ...

Created: 2013-05-29 | Last updated: 2014-01-09

Credits: Antonino Fiannaca Massimo La Rosa

Attributions: Get compound information Simple search

GWAS to biomedical concept (3)

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Genome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow ...

Created: 2013-04-15 | Last updated: 2014-07-14

Credits: Kristina Hettne Harish Dharuri Marco Roos Reinout van Schouwen