Infinium Human Methylation BeadChip
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/960?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

Version History

4 (earliest) Created 22nd Apr 2024 at 11:10 by Helena Rasche

Added/updated 3 files


Open master 432c6e4
help Creators and Submitter
Creators
  • Katarzyna Kamieniecka
  • Khaled Jum'ah
Additional credit

poterlowicz-lab

Submitter
Tools
ewastools
ChIPpeakAnno
clusterProfiler
License
GNU Affero General Public License v3.0 or later
Activity

Views: 47

Created: 22nd Apr 2024 at 11:10

Last updated: 22nd Apr 2024 at 11:10

help Attributions

None

Total size: 20.3 KB
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