Infinium Human Methylation BeadChip
1.0

Workflow Type: Galaxy

The workflow containes the step to perpare the data for and run Galaxy Infinium Human Methylation BeadChip tool that represents many popular algorithms for detecting somatic genetic alterations from genome and exome data

Associated Tutorial

This workflows is part of the tutorial Infinium Human Methylation BeadChip, available in the GTN

Features

Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Katarzyna Kamieniecka, Khaled Jum'ah, poterlowicz-lab

Tutorial Author(s): Katarzyna Kamieniecka, Khaled Jum'ah, Krzysztof Poterlowicz

Tutorial Contributor(s): Björn Grüning, Helena Rasche, Saskia Hiltemann, Katarzyna Kamieniecka, Khaled Jum'ah, Krzysztof Poterlowicz, Nicola Soranzo, kpbioteam, Mélanie Petera, Bérénice Batut

Funder(s): ELIXIR Europe

SEEK ID: https://workflowhub.eu/workflows/1624?version=1

Inputs

ID	Name	Description	Type
R01C02_Green.idat	#main/R01C02_Green.idat	n/a	File
R01C02_Red.idat	#main/R01C02_Red.idat	n/a	File
R02C02_Green.idat	#main/R02C02_Green.idat	n/a	File
R02C02_Red.idat	#main/R02C02_Red.idat	n/a	File
R05C02_Green.idat	#main/R05C02_Green.idat	n/a	File
R05C02_Red.idat	#main/R05C02_Red.idat	n/a	File
R06C02_Green.idat	#main/R06C02_Green.idat	n/a	File
R06C02_Red.idat	#main/R06C02_Red.idat	n/a	File
UCSC Main on Human	#main/UCSC Main on Human	n/a	File
phenotype Table txt file	#main/phenotype Table txt file	n/a	File

Steps

ID	Name	Description
10	Infinium Human Methylation BeadChip	toolshed.g2.bx.psu.edu/repos/kpbioteam/ewastools/minfi_analysis/2.1.0
11	ChIPpeakAnno annoPeaks	toolshed.g2.bx.psu.edu/repos/kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks/0.1.0
12	Cut	Cut1
13	Remove beginning	Remove beginning1
14	Cluster Profiler Bitr	toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0
15	Cluster Profiler GO	toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0

Outputs

ID	Name	Description	Type
Cut on Table of Annotated Peaks	#main/Cut on Table of Annotated Peaks	n/a	File
Differentially Methylated Positions	#main/Differentially Methylated Positions	n/a	File
Differentially Methylated Regions	#main/Differentially Methylated Regions	n/a	File
GO Enrichment Analysis Visualization	#main/GO Enrichment Analysis Visualization	n/a	File
GO Enrichment Analysis of a Gene Set	#main/GO Enrichment Analysis of a Gene Set	n/a	File
Quality Control Plot	#main/Quality Control Plot	n/a	File
Quality Control Report	#main/Quality Control Report	n/a	File
Remove beginning on the cut output	#main/Remove beginning on the cut output	n/a	File
SNPInfo Table	#main/SNPInfo Table	n/a	File
Table of Annotated Peaks	#main/Table of Annotated Peaks	n/a	File
Table of Translated Gene ID's	#main/Table of Translated Gene ID's	n/a	File