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Download data from array express + create ... (1)

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This workflow uses the array express library to download data from the array express repository and creates two separate files. The gene expression and the phenotype files. The files are saved in the directory that the user has to specify in the input. NOTE: The library(ArrayExpress) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

Get differentially expressed genes for Arr... (1)

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****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133a.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow. Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for ...

Created: 2013-11-04

Credits: Eleni

Get differentially expressed genes for Arr... (1)

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****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133b.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow. Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for ...

Created: 2013-11-04

Credits: Eleni

get promoter region + operate on genomic i... (1)

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Finds the overlap between two datasets which contain genomic information (e.g. [gene id], chromosome name, gene start, gene end), plus some statistics. Returns rows of file_1 which overlap with the second file. A kolmogorov smirnov test is applied between the list that overlaps and the one that does not. NOTE: The library(GenomicRanges) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni