Infinium Human Methylation BeadChip

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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

Thanks to...

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

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

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1165?version=2

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

Version History

1.0 (latest) Created 16th Jul 2024 at 14:06 by Helena Rasche

Added/updated 4 files


Open master 3329567

4.0 (earliest) Created 25th Jun 2024 at 11:05 by Helena Rasche

Added/updated 4 files


Frozen 4.0 8a9a246
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
ewastools
ChIPpeakAnno
clusterProfiler
License
GNU Affero General Public License v3.0 or later
Activity

Views: 446   Downloads: 136

Created: 25th Jun 2024 at 11:05

Last updated: 25th Jun 2024 at 11:05

help Attributions

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Total size: 177 KB
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