X
(Package: ccTutorial) :
ExpressionSet containing ChIP-chip data
Preprocessed ChIP-chexpression data from M. musculus brain and heart cells. H3K4me3 ChIP and input samples were hybridized to a set of four custom NimbleGen microarrays with non-overlapping sets of 390k reporters each. The results were preprocessed per array type and the result fold changes were combinded via rbind afterwards, resulting in this ExpressionSet with 1.5m reporters.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: X
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0 images
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arrayGenesToProbeSets
(Package: ccTutorial) :
Mapping of Ensembl mm9 genes to Affymetrix Mouse 430v2 probe sets
This is a mapping of Ensembl mm9 genes to Affymetrix Mouse 430v2 probe sets. Onyl Ensembl mm9 genes that mapped at least one probe set on the array are included in the list. This mapping was created using biomaRt on 27 May 2008. Users can create this list themselves and the supplement contains the source code for doing this. For convenience sake, this object is given as a data object.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: arrayGenesToProbeSets
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Preprocessed expression data for five M. musculus tissues. Samples were hybridized to Affymetrix's mouse430v2 array platform, preprocessed using the MAS5 method, as implemented in Bioconductor's package affy.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: barreraExpressionX
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chersX
(Package: ccTutorial) :
List of found ChIP-enriched regions
This is the list of found ChIP-enriched regions. The package contains all the data to recreate the list and this list is merely given for convenience sake.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: chersX
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mm9.g2p
(Package: ccTutorial) :
Mapping of Ensembl mm9 genes and reporter match positions
a list holding for each mm9 gene annotated in the Ensembl database, which reporter - if any - have been mapped into its upstream or transcribed region. Users can create this list themselves and the manuscript contains the source code for doing this. For convenience sake, this list is also given as a data object.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: mm9.g2p
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1 images
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mm9.gene2GO
(Package: ccTutorial) :
GO annotation of Ensembl mm9 genes
a list holding the GO terms annotated for each mm9 gene annotated in Ensembl, as retrieved using biomaRt. Users can create this list themselves and the supplement contains the source code for doing this. For convenience sake, this is also given as a data object.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: mm9.gene2GO
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0 images
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mm9genes
(Package: ccTutorial) :
data frame of mm9 genes in Ensembl
~~ A concise (1-5 lines) description of the dataset. ~~
● Data Source:
BioConductor
● Keywords: datasets
● Alias: mm9genes
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0 images
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probeAnno
(Package: ccTutorial) :
probeAnno object holding mapping of reporters to genomic positions
This object of class probeAnno holds the mapping of the reporters on the tiling microarrays to positions in the mouse genome (assembly: mm9).
● Data Source:
BioConductor
● Keywords: datasets
● Alias: probeAnno
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