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Items tagged with "r" (29)
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Created: 13/03/08 @ 14:38:03 | Last updated: 16/02/09 @ 16:41:29
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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Created: 16/02/09 @ 16:32:36 | Last updated: 16/02/09 @ 16:42:10
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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 ...
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Created: 15/04/08 @ 15:37:42 | Last updated: 01/07/08 @ 17:21:18
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 02/07/08 @ 11:24:12 | Last updated: 02/07/08 @ 11:28:21
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 13/02/09 @ 09:05:35 | Last updated: 13/02/09 @ 09:08:20
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
...
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Created: 15/03/10 @ 08:43:31
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script
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Created: 19/03/10 @ 10:26:34 | Last updated: 19/03/10 @ 10:29:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
A workflow to invoke a Gene Pattern module using an R script. Note that a FTP URL for the data to be analysed is required, not the data itself!
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Created: 22/03/10 @ 09:56:03
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow performs key driver analysis and displays the results in Cytoscape.
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Created: 26/03/10 @ 17:20:14
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow parameterises an SBML model generated by the qualitative SBML model construction workflow
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Created: 26/11/10 @ 15:13:46 | Last updated: 26/11/10 @ 15:13:48
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License: Creative Commons Attribution 3.0 Unported License
This workflow uses an R service running on localhost to calculate sin(0.45)
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Created: 26/11/10 @ 15:44:15 | Last updated: 26/11/10 @ 15:44:18
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License: Creative Commons Attribution 3.0 Unported License
Checks what the logical_input is in R. For an logical_input of
TRUE - is_false should be FALSE and is_true TRUE
FALSE - is_false should be TRUE and is_true FALSE
For any other input values, is_false and is_true should both be NA
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Created: 26/11/10 @ 16:47:02 | Last updated: 26/11/10 @ 16:47:04
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License: Creative Commons Attribution 3.0 Unported License
This workflow determines the lower case version of the input string.
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Created: 26/11/10 @ 17:06:00 | Last updated: 26/11/10 @ 17:06:03
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License: Creative Commons Attribution 3.0 Unported License
The workflow returns a list containing the logical inversion of the logical vector input
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Created: 26/11/10 @ 17:21:45 | Last updated: 26/11/10 @ 17:21:48
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License: Creative Commons Attribution 3.0 Unported License
This workflow takes a list of numbers and outputs a list containing the squares of the numbers and the sum of the numbers in the list
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Created: 26/11/10 @ 17:34:05 | Last updated: 26/11/10 @ 17:34:08
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License: Creative Commons Attribution 3.0 Unported License
This workflow takes a list of integer values and returns a list containing the square of the input list's elements, and the sum of the input list's elements.
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Created: 26/11/10 @ 18:06:35 | Last updated: 26/11/10 @ 18:06:37
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License: Creative Commons Attribution 3.0 Unported License
The workflow takes a list of strings and outputs a list contains the lower-cased versions of the input elements, and also a concatenation of the input elements
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Created: 29/11/10 @ 10:15:37 | Last updated: 29/11/10 @ 10:15:40
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License: Creative Commons Attribution 3.0 Unported License
This workflow takes a list of integer values and returns a list containing 100 modulus the list's elements, and the sum of the input list's elements.
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Created: 29/11/10 @ 12:40:12 | Last updated: 29/11/10 @ 13:13:11
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License: Creative Commons Attribution 3.0 Unported License
This workflow produces a PNG plot on the figure port.
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Created: 13/12/10 @ 16:28:15 | Last updated: 13/12/10 @ 16:28:42
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License: Creative Commons Attribution 3.0 Unported License
This workflow fetches the details of the countries in the world and then uses R to produce a histogram of the log of their population
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Created: 21/09/11 @ 18:10:49 | Last updated: 21/09/11 @ 18:10:53
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License: Creative Commons Attribution 3.0 Unported License
This workflow fetches the details of the countries in the world and then uses R to produce a histogram of the log of their population
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Created: 06/10/11 @ 03:54:30 | Last updated: 06/10/11 @ 16:32:18
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Functionally identical to the original. I tried to upload a version with annotation, but somehow the notes didn't make it to myExperiment.
From the prior verion:
This workflow accepts city and country names as user-supplied input. These value are supplied to the GetWeather webservice (http://www.webservicex.net/globalweather.asmx?WSDL), which returns an XML record of location and weather info for each recognized city. (See the uploaded photo "weather example")
The XML returned fr...
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Created: 02/07/08 @ 11:30:06 | Last updated: 04/02/10 @ 11:41:11
No description
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Created: 11/12/08 @ 12:02:47 | Last updated: 22/01/09 @ 09:06:26
This package contains all elements required to run the RShell use case "Mapping oligonucleotides to an assembly"
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Created: 25/03/10 @ 20:31:36 | Last updated: 26/03/10 @ 17:23:44
A pack of workflows for the construction, parameterisation, optimisation and simulation of SBML models.
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Created: 13/12/10 @ 10:44:04 | Last updated: 13/12/10 @ 16:28:58
Small workflows illustrating how R can be used within Taverna services
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Created: 06/10/11 @ 03:06:32 | Last updated: 06/10/11 @ 04:15:33
This pack contains the workflows and supplemental files that I created for a project in IST600 - eScience and eResearch Workflows.
This workflow accepts city and country names as user-supplied input. These value are supplied to the GetWeather webservice (http://www.webservicex.net/globalweather.asmx?WSDL), which returns an XML record of location and weather info for each recognized city. (See the uploaded photo "weather example")
The XML returned from GetWeather is then searched u...
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Created: 01/04/11 @ 09:12:28 | Last updated: 01/04/11 @ 09:12:40
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Attributions: License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list processed for Human gene expression CEL files relating to the: Impact of NRSF variant over-expression in SK-N-AS human neuroblastoma cells (http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-GEOD-22467&expandefo=on).
The CEL files were analysed using the MADAT Taverna workflow available on myExperiment:
http://www.myexperiment.org/workflows/2002.html
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Created: 06/10/11 @ 03:27:24 | Last updated: 06/10/11 @ 03:27:29
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License: Creative Commons Attribution 3.0 Unported License
This screenshot shows the "Elevation plot..." workflow with the nested workflows compact.
img, #cubbies-overlay{ -moz-transition-property: margin, box-shadow, z-index; -moz-transition-duration: 0.1s; -webkit-transition-property: margin, box-shadow, z-index; -webkit-transition-duration: 0.1s; }
.cubbies-selected{ z-index: 9999; box-shadow: 3px 3px 8px -1px blue !important; cursor: pointer !important; margin: -3px 3px 3px -3px; }
.cubbies-selected:active{ box-shadow: 2px 2px 5px -1...
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Created: 06/10/11 @ 03:32:17 | Last updated: 06/10/11 @ 03:32:19
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License: Creative Commons Attribution 3.0 Unported License
This screenshot shows what output of the "Elevation plot..." workflow looks like.
img, #cubbies-overlay{ -moz-transition-property: margin, box-shadow, z-index; -moz-transition-duration: 0.1s; -webkit-transition-property: margin, box-shadow, z-index; -webkit-transition-duration: 0.1s; }
.cubbies-selected{ z-index: 9999; box-shadow: 3px 3px 8px -1px blue !important; cursor: pointer !important; margin: -3px 3px 3px -3px; }
.cubbies-selected:active{ box-shadow: 2px 2px 5px -1px darkb...
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