<?xml version="1.0" encoding="UTF-8"?>

<module name="microarray">
		
	<category name="Normalisation" color="#d5c796">
		<tool runtime="R-2.12"><resource>norm-affy.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-affy-exon.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-affy-gene.R</resource></tool>
		<tool runtime="R-2.15"><resource>norm-affy-snp.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-agilent-one-color.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-agilent.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-agilent-miRNA.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-cdna.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-illumina.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-illumina-lumi.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11"><resource>norm-illumina-methylumi.R</resource></tool>
		<tool runtime="R-2.15"><resource>norm-illumina-SNP.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-prenormalized.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-prenormalized-affy.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-lme.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11"><resource>norm-combat.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-chip-average.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-gene-average.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-specific-samples.R</resource></tool>
		<tool runtime="R-2.12"><resource>norm-specific-genes.R</resource></tool>
	</category>
	
	<category name="Quality control" color="#e7df70">
		<tool runtime="R-2.12"><resource>qc-affy.R</resource></tool>
		<tool runtime="R-2.12"><resource>qc-affy-rle-nuse.R</resource></tool>
		<tool runtime="R-2.12"><resource>qc-affy-exon-rle-nuse.R</resource></tool>
		<tool runtime="R-2.12"><resource>qc-illumina.R</resource></tool>
		<tool runtime="R-2.12"><resource>qc-agilent.R</resource></tool>
		<tool runtime="R-2.12"><resource>qc-agilent-one-color.R</resource></tool>
		<tool runtime="R-2.12"><resource>qc-cdna.R</resource></tool>
	</category>
	
	<category name="Preprocessing" color="#d59f45">
		<tool runtime="R-2.12"><resource>filter-expression.R</resource></tool>
		<tool runtime="R-2.12"><resource>filter-flags.R</resource></tool>
		<tool runtime="R-2.12"><resource>filter-sd.R</resource></tool>
		<tool runtime="R-2.12"><resource>filter-iqr.R</resource></tool>
		<tool runtime="R-2.12"><resource>filter-cv.R</resource></tool>
		<tool runtime="R-2.12"><resource>filter-by-column-term.R</resource></tool>
		<tool runtime="R-2.12"><resource>filter-by-column-value.R</resource></tool>
		<tool runtime="R-2.12"><resource>impute.R</resource></tool>
		<tool runtime="R-2.12"><resource>na-omitted.R</resource></tool>
		<tool runtime="R-2.12"><resource>dichotomize-continious-data.R</resource></tool>
	</category>
	
	<category name="Statistics" color="#e7881c">
		<tool runtime="R-2.12"><resource>stat-one-group.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-two-groups.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-ROTS.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-sam.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-several-groups.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-linear-modelling.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-linear-modelling-designmat.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-proportions.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-correlate-with-phenodata.R</resource></tool>
		<tool runtime="R-2.12"><resource>correlation-analysis-mirna.R</resource></tool> 
		<tool runtime="R-2.12"><resource>stat-timeseries.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-chisq-snp.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-adjust-pvalues.R</resource></tool>
		<tool runtime="R-2.12"><resource>ordination-pca.R</resource></tool>
		<tool runtime="R-2.12"><resource>ordination-ca.R</resource></tool>
		<tool runtime="R-2.12"><resource>ordination-nmds.R</resource></tool>
		<tool runtime="R-2.12"><resource>estimate-samplesize.R</resource></tool>
		<tool runtime="R-2.12"><resource>sample-size-with-bh.R</resource></tool>
		<tool runtime="R-2.12"><resource>up-down-analysis-mirna.R</resource></tool>
	</category>
	
	<category name="Clustering" color="#d53833">
		<tool runtime="R-2.12"><resource>classification-knn.R</resource></tool>
		<tool runtime="R-2.12"><resource>cluster-hierarchical.R</resource></tool>
		<tool runtime="R-2.12"><resource>cluster-kmeans.R</resource></tool>
		<tool runtime="R-2.12"><resource>cluster-kmeans-testK.R</resource></tool>
		<tool runtime="R-2.12"><resource>cluster-qt.R</resource></tool>
		<tool runtime="R-2.12"><resource>cluster-som.R</resource></tool>
		<tool runtime="R-2.12"><resource>classification.R</resource></tool>
	</category>
	
	<category name="Annotation" color="#80a3b7">
		<tool runtime="R-2.12"><resource>annotate-genelist2html.R</resource></tool>
		<tool runtime="R-2.12"><resource>annotate-add-to-data.R</resource></tool>
		<tool runtime="R-2.12"><resource>add-locations-to-data.R</resource></tool>
		<tool runtime="R-2.12"><resource>annotate-miRNA-targets.R</resource></tool> 
		<tool runtime="R-2.12"><resource>annotate-agilent-miRNA.R</resource></tool> 
	</category>
	
	<category name="Pathways" color="#0177b7">
		<tool runtime="R-2.12"><resource>stat-hyperG-GO.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-hyperG-KEGG-PFAM.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-hyperG-safe.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-hyperG-cytoband.R</resource></tool>
		<tool runtime="R-2.12"><resource>stat-geneset.R</resource></tool>
		<tool runtime="R-2.12"><resource>pathways-mirna-hyperg-go.R</resource></tool> 
		<tool runtime="R-2.12"><resource>pathways-mirna-hyperg-kegg.R</resource></tool> 
		<tool runtime="beanshell" module="common"><resource>annotate-cpdb.bsh</resource></tool>
		<tool runtime="beanshell"><resource>annotate-intact.bsh</resource></tool>
		<tool runtime="beanshell"><resource>annotate-reactome.bsh</resource></tool>
	</category>

	<category name="Promoter analysis" color="#629a9b">
		<tool runtime="R-2.12"><resource>promoter-tfbs.R</resource></tool>
		<tool runtime="R-2.12"><resource>promoter-tfbs-cosmo.R</resource></tool>
		<tool runtime="R-2.12"><resource>promoter-cbust.R</resource></tool>
		<tool runtime="R-2.12"><resource>promoter-retrprom.R</resource></tool>
	</category>

	<category name="Copy number aberrations" color="#c0d2de">
		<tool runtime="R-2.12"><resource>import-soft2.R</resource></tool>
		<tool runtime="R-2.12"><resource>acgh-import-from-cangem.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-normalize.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-plot-profile.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11"><resource>acgh-smooth.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11"><resource>acgh-segment.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-call-aberrations.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-identify-regions.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-plot-frequencies.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-cluster.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-group-test.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-survival-test.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-plot-survival.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-convert-from-probes-to-genes.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-pathways-go.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-match-probes.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-plot-combined-profile.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-expression-test.R</resource></tool>	
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-plot-combined-expression.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11"><resource>acgh-fetch-probe-positions-from-cangem.R</resource></tool>
		<tool runtime="R-2.12"><resource>acgh-fetch-probe-positions-from-geo.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-add-cytobands.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-count-overlapping-cnvs.R</resource></tool>
	</category>

	<category name="Visualisation" color="#a49900">
		<tool runtime="R-2.12"><resource>plot-idiogram.R</resource></tool>
		<tool runtime="R-2.12"><resource>plot-chrom-pos.R</resource></tool>
		<tool runtime="R-2.12"><resource>plot-volcano.R</resource></tool>
		<tool runtime="R-2.12"><resource>plot-volcano-data-exists.R</resource></tool>
		<tool runtime="R-2.12"><resource>plot-boxplot.R</resource></tool>
		<tool runtime="R-2.12"><resource>plot-dendrogram.R</resource></tool>
		<tool runtime="R-2.12"><resource>plot-histogram.R</resource></tool>
		<tool runtime="R-2.12"><resource>plot-corrgram.R</resource></tool>
		<tool runtime="R-2.12"><resource>plot-heatmap.R</resource></tool>
	</category>

	<category name="Utilities" color="#83010b">
		<tool runtime="R-2.12"><resource>search-correlation.R</resource></tool>
		<tool runtime="R-2.12"><resource>search-queryword.R</resource></tool>
		<tool runtime="R-2.12"><resource>search-coordinates.R</resource></tool>
		<tool runtime="R-2.12"><resource>merge-tables.R</resource></tool>
		<tool runtime="R-2.12"><resource>merge-datasets.R</resource></tool>
		<tool runtime="R-2.12"><resource>extract-genes-from-clustering.R</resource></tool>
		<tool runtime="R-2.12"><resource>extract-genes-from-go.R</resource></tool>
		<tool runtime="R-2.12"><resource>extract-genes-from-kegg.R</resource></tool>
		<tool runtime="R-2.12" module="common"><resource>extract-samples-from-dataset.R</resource></tool>		
		<tool runtime="R-2.12"><resource>extract-genes-from-stattest.R</resource></tool>
		<tool runtime="R-2.12"><resource>extract-genes.R</resource></tool>
		<tool runtime="R-2.12"><resource>calculate-fold-change.R</resource></tool>
		<tool runtime="R-2.12"><resource>average-replicates.R</resource></tool>
		<tool runtime="R-2.12"><resource>combine-probes-to-genes.R</resource></tool>
		<tool runtime="R-2.12"><resource>change-interpretation.R</resource></tool>
		<tool runtime="R-2.12"><resource>generate-phenodata.R</resource></tool>
		<tool runtime="R-2.12"><resource>delete-columns.R</resource></tool>
		<tool runtime="R-2.12"><resource>calculate-descriptive-statistics.R</resource></tool>
		<tool runtime="R-2.12"><resource>sort-samples.R</resource></tool>
		<tool runtime="R-2.12"><resource>sort-genes.R</resource></tool>
		<tool runtime="R-2.12"><resource>sampling.R</resource></tool>
		<tool runtime="R-2.12"><resource>export-tab2mage.R</resource></tool>
		<tool runtime="R-2.12"><resource>export-soft.R</resource></tool>
		<tool runtime="R-2.12"><resource>import-soft2.R</resource></tool>
		<tool runtime="R-2.12"><resource>import-ArrayExpress.R</resource></tool>
		<tool runtime="R-2.12"><resource>intersect-lists.R</resource></tool>
	</category>
	
	<category name="Hidden" hidden="true" color="#0">
		<tool runtime="R-2.12"><resource>test.R</resource></tool>
		<tool runtime="R-2.12"><resource>no-operation.R</resource></tool>
		<tool runtime="R-2.12"><resource>echo.R</resource></tool>
		<tool runtime="R-2.12"><resource>fail.R</resource></tool>
		<tool runtime="R-2.12"><resource>input-output.R</resource></tool>
		<tool runtime="R-2.12"><resource>simple-input-output.R</resource></tool>
		<tool runtime="R-2.12"><resource>data-throughput.R</resource></tool>
		<tool runtime="R-2.12"><resource>sleep.R</resource></tool>
		<tool runtime="R-2.12"><resource>input-sleep-output.R</resource></tool>
	</category>
</module>
