hES
(Package: ClueR) :
Human embryonic stem cell phosphoproteomics data
The data object contains a time-course phosphoprotoemics profiling of the human embryonic stem cells through differentiation. The differentiation is induced by using PMA and the time points of 30m, 1hr, 6hrs, and 24hrs are measured and the ratio are taken against 0m. For details please refer to the article: Rigbolt et al. Sci Signal. 4(164):rs3, 2011
● Data Source:
CranContrib
● Keywords:
● Alias: hES
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0 images
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Pathways.KEGG
(Package: ClueR) :
KEGG pathway annotations
The data object contains the annotations of KEGG pathways.
● Data Source:
CranContrib
● Keywords:
● Alias: Pathways.KEGG
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0 images
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enrichmentTest
(Package: ClueR) :
Fisher's exact test-based enrichment test
Takes a vector of names representing phosphorylation sites that are partitioned in the same cluster and an kinase-substrate annotation. Test for enrichment of the kinase based on the name vector.
● Data Source:
CranContrib
● Keywords:
● Alias: enrichmentTest
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0 images
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clustOptimal
(Package: ClueR) :
Generate optimal clustering
Takes a clue output and generate the optimal clustering of the time-course data.
● Data Source:
CranContrib
● Keywords:
● Alias: clustOptimal
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2 images
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runClue
(Package: ClueR) :
Run CLUster Evaluation
Takes in a time-course matrix and test for enrichment of the clustering using cmeans or kmeans clustering algorithm with a reference annotation.
● Data Source:
CranContrib
● Keywords:
● Alias: runClue
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2 images
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The data object contains the annotations of reactome pathways.
● Data Source:
CranContrib
● Keywords:
● Alias: Pathways.reactome
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0 images
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PhosphoSite.human
(Package: ClueR) :
PhosphoSitePlus annotations for human
The data object contains the annotations of kinases and their conrresponding substrates as phosphorylation sites in human. It is extracted from the PhosphoSitePlus database. For details of PhosphoSitePlus, please refer to the article: Hornbeck et al. Nucleic Acids Res. 40:D261-70, 2012
● Data Source:
CranContrib
● Keywords:
● Alias: PhosphoSite.human
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0 images
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PhosphoSite.mouse
(Package: ClueR) :
PhosphoSitePlus annotations for mouse
The data object contains the annotations of kinases and their conrresponding substrates as phosphorylation sites in mouse. It is extracted from the PhosphoSitePlus database. For details of PhosphoSitePlus, please refer to the article: Hornbeck et al. Nucleic Acids Res. 40:D261-70, 2012
● Data Source:
CranContrib
● Keywords:
● Alias: PhosphoSite.mouse
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0 images
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Takes a clustering object generted by cmeans or kmeans algorithm and determine the enrichment of each cluster and then the overall enrichment of this clustering object based on an annotation file.
● Data Source:
CranContrib
● Keywords:
● Alias: clustEnrichment
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0 images
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fuzzPlot
(Package: ClueR) :
Visualize fuzzy clustering results
Takes in a time-course matrix and its clustering results as a cmeans clustering object. Produce a plot to visualize the clustering results.
● Data Source:
CranContrib
● Keywords:
● Alias: fuzzPlot
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1 images
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