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Human Gene expression data -

Created: 2011-04-01 09:12:28 | Last updated: 2011-04-01 09:12:40

Credits: Saeedeh

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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Workflow compact

Created: 2011-10-06 03:27:24 | Last updated: 2011-10-06 03:27:29

Credits: Chrisser

License: Creative Commons Attribution 3.0 Unported License

File type: JPEG image

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"Elevation plot..." example output

Created: 2011-10-06 03:32:17 | Last updated: 2011-10-06 03:32:19

Credits: Chrisser

License: Creative Commons Attribution 3.0 Unported License

File type: JPEG image

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Microarray data analysis using R

Created: 2008-07-02 11:30:06 | Last updated: 2010-02-04 11:41:11

3 items in this pack

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Package: mapping oligonucleotides to an assembly

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

5 items in this pack

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Systematic integration of experimental data and mode...

Created: 2010-03-25 20:31:36 | Last updated: 2010-03-26 17:23:44

5 items in this pack

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Example R workflows

Created: 2010-12-13 10:44:04 | Last updated: 2010-12-13 16:28:58

10 items in this pack

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Find elevation given city and country names

Created: 2011-10-06 03:06:32 | Last updated: 2011-10-06 04:15:33

7 items in this pack

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AffyArrayQualityAnalysis (2)

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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...

Created: 2008-03-13 | Last updated: 2009-02-16

Credits: Pieter Neerincx Philipg

AffyArrayNormalization (2)

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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 ...

Created: 2009-02-16 | Last updated: 2009-02-16

Credits: Pieter Neerincx Philipg

Identification of differential genes using... (2)

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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.

Created: 2008-04-15 | Last updated: 2008-07-01

Credits: Peter Li

Identification of differential genes using... (1)

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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...

Created: 2008-07-02 | Last updated: 2008-07-02

Credits: Peter Li

Mapping OligoNucleotides to an assembly (7)

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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: Wassinki Pieter Neerincx

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

Calculating frequencies of gene expression... (1)

This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script

Created: 2010-03-15

Credits: Peter Li

Invocation of Gene Pattern modules using R (1)

 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!

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Peter Li

Sage bionetwork demo workflow (1)

This workflow performs key driver analysis and displays the results in Cytoscape.

Created: 2010-03-22

Credits: Peter Li

SBML model parameterisation (1)

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This workflow parameterises an SBML model generated by the qualitative SBML model construction workflow

Created: 2010-03-26

Credits: Peter Li

A Basic example R workflow (3)

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This workflow uses an R service running on localhost to calculate sin(0.45)

Created: 2010-11-26 | Last updated: 2014-08-20

Credits: Alan Williams

R logical workflow (1)

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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

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R string workflow (1)

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This workflow determines the lower case version of the input string.

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R logical vector workflow (1)

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The workflow returns a list containing the logical inversion of the logical vector input

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R integer vector example (1)

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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.

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R string vector example (1)

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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

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R integer vector example (1)

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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.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: Alan Williams

R PNG-value example (2)

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This workflow produces a PNG plot on the figure port.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: Alan Williams

Population histogram in R (1)

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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

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: Chrisser

Attributions:

Elevation plot v.2 (2)

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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...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Chrisser

Convert Taverna list of RExpr to R list - v2 (2)

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This workflow accepts a Taverna list of arbitrary R expressions and returns a single R expression representing an R list containing the original expressions. This workflow relies on the current Taverna behaviour of an R expression being represented by a list of strings containing the deparsed expression. If this changes, this workflow will likely break. The first BeanShell converts each R expression (actually a list of strings) to a single string. This uses implicit iteration to do this for...

Created: 2013-09-04 | Last updated: 2013-10-14

Credits: Jon Giddy BioVeL

Print R expression (3)

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This is a very small nested workflow to convert an R expression to the same textual representation that you see displayed when using the R command line.

Created: 2013-09-05 | Last updated: 2013-10-16

Credits: Jon Giddy

Increment an integer (1)

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This workflow uses R to increment the input integer

Created: 2014-10-03

Credits: Alan Williams

Online PubMed author search and geographic... (2)

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This workflow retrieves bibliographic data for a single author using the PMC Europe RESTful Web service and visualizes the geographic distribution of this author's and their co-authors' geographic distribution using the rworldmap package. This is version 2.0 of this workflow, incorporating changes to the Web service allowing up to 1,000 records to be retrieved at once, using the pageSize parameter.

Created: 2015-08-19 | Last updated: 2015-09-07

Credits: Magnus Palmblad Arzu Tugce Guler

Visualize Geographical Bias between PubMed... (3)

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This workflow analyzes the scientific output, as documented by PubMed, geographically. The workflow takes as input the PubMed data in XML and the ISO 3166-1 and ISO 3166-3 country lists. The XML files can contain any subset from two specific PubMed searches. for example for two different journals in the same field. The XPath components extract author affiliations, and feed these to a series of Beanshell components that match these with countries in the ISO standard. This data is then fed to ...

Created: 2015-09-10 | Last updated: 2015-09-10

Credits: Magnus Palmblad Arzu Tugce Guler

Author Publications and Citations by Year (2)

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This small workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService) to count the number of publications and citations per year for one author. Two Web service calls are made. First, we searchPublications to retrieve the bibliographic records for all published work of a single author. Then, we getCitations to extract the year of all articles citing the work of this author. A conditional XPath is here used to only look up citing articles for cited work...

Created: 2015-09-14 | Last updated: 2015-09-17

Credits: Magnus Palmblad

Author to Wordcloud (3)

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This small workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService). The workflow searches the publications of an author, extracts the abstracts, counts the word frequencies and plot a wordcloud using the R package of the same name. The Rshell plot_wordcloud also applies text mining operations (transformation to lower case, removing punctuation, stripping whitespace and removing English stopwords) using the R package tm.

Created: 2015-12-02 | Last updated: 2015-12-07

Credits: Magnus Palmblad

Author Publications and Citations by Year ... (1)

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This small workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService) to count the number of publications and citations per year for one author. Two REST calls are made. First, we "searchPublications" to retrieve the bibliographic records for all published work of a single author. Then, we "getCitations" to extract the year of all articles citing the work of this author. A conditional JSONPath is here used to only look up citing articles for cited work...

Created: 2016-05-09

Credits: Magnus Palmblad

Author Publications and Citations by Year ... (2)

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This small workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService) to count the number of publications and citations per year for one author. Two REST calls are made. First, we "searchPublications" to retrieve the bibliographic records for all published work of a single author. Then, we "getCitations" to extract the year of all articles citing the work of this author. A conditional XPath is here used to only look up citing articles for cited work, i...

Created: 2016-05-09 | Last updated: 2016-05-09

Credits: Magnus Palmblad