Tag Results

Items tagged with "biomart" (17)

Note: some items may not be visible to you, due to viewing permissions.


Packs (2)
Creator

Pack Package: mapping oligonucleotides to an assembly


Created: 2008-12-11 12:02:47 | Last updated: 2009-01-22 09:06:26

This package contains all elements required to run the RShell use case "Mapping oligonucleotides to an assembly"  

5 items in this pack

Comments: 0 | Viewed: 240 times | Downloaded: 85 times

Tags:

Creator

Pack HD chromatin analysis


Created: 2013-08-28 12:17:37 | Last updated: 2016-10-28 15:02:27

This pack is comprised by all workflows used for the integration and the analysis of Huntington's Disease (HD) gene expression data and epigenetic datasets in order to establish links between HD and epigenetic regulation in disease.  

6 items in this pack

Comments: 0 | Viewed: 83 times | Downloaded: 18 times

Tags:

Workflows (15)

Workflow BiomartAndEMBOSSAnalysis (4)

Thumb
Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2009-09-15 | Last updated: 2015-01-26

Uploader

Workflow Mapping OligoNucleotides to an assembly (7)

Thumb
Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ...

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

Credits: User Wassinki User Pieter Neerincx

Attributions: Workflow Blat against ENSEMBLE Danio_rerio_Genome Workflow BlatBlastCombi Workflow Blast against ENSEMBLE Danio_rerio_Genome Workflow AppendToFile Blob Test Input for Mapping oligonucleotides to an assembly Blob Input for Mapping oligonucleotides to an assembly

Workflow Biomart Protein Sequence Retrieval (1)

Thumb
This workflow queries Biomart to retrieve the Ensembl gene id, protein id, gene name, description and amino acid sequence from the Ensembl Homo sapiens dataset. The user needs to specify a defined chromosomal region i.e. Chromo = 1, Start = 100000000, End = 250000000. This returns all unique entries in FASTA format.

Created: 2009-03-09

Credits: User Kieren Lythgow

Workflow BioMart and Emboss Analysis (T2) (1)

Thumb
This is the Taverna 2 version of the Biomart and Emboss Analysis workflow http://www.myexperiment.org/workflows/158   Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned. Previous versions of this workflow only returned sequences with an ID mapped to a MIM_morbid_accession. This was primarily to reduce the numbe...

Created: 2009-09-15

Credits: User Katy Wolstencroft User Alan Williams

Attributions: Workflow BiomartAndEMBOSSAnalysis

Workflow Biomart and Blast (1)

Thumb
Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart) Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: Workflow BLAST using DDBJ service

Workflow Biomart and Blast with concatinated gene id (1)

Thumb
Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). Finally (to showcase Taverna pipelining) - the Ensembl gene ID is added as a prefix on the BLAST report. Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: Workflow BLAST using DDBJ service Workflow Biomart and Blast

Workflow BiomartAndEMBOSSDisease (4)

Thumb
This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned. Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2011-01-27 | Last updated: 2012-09-04

Credits: User Katy Wolstencroft User Alan Williams

Attributions: Workflow BiomartAndEMBOSSAnalysis

Workflow Find PRIDE experiments by GO (1)

Thumb
Find PRIDE experiments in Human with related information like Cell Type and Tissue location filtering results by Gene Ontology terms. This is an example of how to use the PRIDE Biomart service in Taverna. Many other options are possible by modifying the filters and attributes of this service.

Created: 2011-05-29 | Last updated: 2011-05-29

Credits: User Rafael C. Jimenez

Workflow Find Reactome pathways and reactions by GO (1)

Thumb
Find Reactome pathways and reactions (names and accessions) in Human querying by a Gene Ontology term. This is an example of how to use the Reactome Biomart service in Taverna. Many other possibilities are possible by modifying the filters and attributes options of the service.

Created: 2011-05-29 | Last updated: 2011-05-29

Credits: User Rafael C. Jimenez

Workflow Biomart SNP (1)

Thumb
Normal 0 false false false EN-US X-NONE AR-SA /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyl...

Created: 2011-06-20 | Last updated: 2011-07-05

Credits: User Yosr Bouhlal

Workflow BiomartAndEMBOSSDisease (2)

Thumb
This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2011-07-12 | Last updated: 2012-03-19

Credits: User Katy Wolstencroft

Attributions: Workflow BiomartAndEMBOSSDisease

Workflow Biomart datasets for the Ensembl Genes mar... (1)

Thumb
Retrieve Biomart datasets for the Ensembl Genes mart service (one dataset per specie).

Created: 2011-10-03

Credits: User Rafael C. Jimenez

Workflow Find Orthologs for proteins in Ensembl (1)

Thumb
Find Orthologs for proteins in Ensembl using biomart.

Created: 2011-10-03 | Last updated: 2011-10-03

Credits: User Rafael C. Jimenez

Uploader

Workflow Map genes to chromosomal location (1)

Thumb
This workflow maps a gene list to the genome using the biomart service, and afterwards computes a promoter region for each gene. The user needs to define the promoter region to be computed. The direction that a gene is transcribed is being taken into account in the "compute_promoter_region_with_strand" component. The variable "strand" is responsible for that. NOTE: The library(biomaRt) is a prerequisite for this workflow

Created: 2013-11-04

Credits: User Eleni

Uploader

Workflow Map genes to chromosomal location for T2WEB (1)

Thumb
This workflow maps a gene list on the genome using the biomart service. IMPORTANT NOTE: Keep in mind that for uploading files on t2web, you need to wait few minutes before executing the workflow. That's essential because the file needs first to be uploaded on the server.

Created: 2013-11-04

Credits: User Eleni

What is this?

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/535


Alternative Formats

HTML
RDF
XML