Infinium Human Methylation BeadChip
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Download RO-CrateThe 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...
Tutorial Author(s): Katarzyna Kamieniecka, Khaled Jum'ah, Krzysztof Poterlowicz
Workflow Author(s): Katarzyna Kamieniecka, Khaled Jum'ah, poterlowicz-lab
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| R01C02_Green.idat | #main/R01C02_Green.idat | n/a |
|
| R01C02_Red.idat | #main/R01C02_Red.idat | n/a |
|
| R02C02_Green.idat | #main/R02C02_Green.idat | n/a |
|
| R02C02_Red.idat | #main/R02C02_Red.idat | n/a |
|
| R05C02_Green.idat | #main/R05C02_Green.idat | n/a |
|
| R05C02_Red.idat | #main/R05C02_Red.idat | n/a |
|
| R06C02_Green.idat | #main/R06C02_Green.idat | n/a |
|
| R06C02_Red.idat | #main/R06C02_Red.idat | n/a |
|
| UCSC Main on Human | #main/UCSC Main on Human | n/a |
|
| phenotype Table txt file | #main/phenotype Table txt file | n/a |
|
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 |
|
| Differentially Methylated Positions | #main/Differentially Methylated Positions | n/a |
|
| Differentially Methylated Regions | #main/Differentially Methylated Regions | n/a |
|
| GO Enrichment Analysis Visualization | #main/GO Enrichment Analysis Visualization | n/a |
|
| GO Enrichment Analysis of a Gene Set | #main/GO Enrichment Analysis of a Gene Set | n/a |
|
| Quality Control Plot | #main/Quality Control Plot | n/a |
|
| Quality Control Report | #main/Quality Control Report | n/a |
|
| Remove beginning on the cut output | #main/Remove beginning on the cut output | n/a |
|
| SNPInfo Table | #main/SNPInfo Table | n/a |
|
| Table of Annotated Peaks | #main/Table of Annotated Peaks | n/a |
|
| Table of Translated Gene ID's | #main/Table of Translated Gene ID's | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:06 by Helena Rasche
Added/updated 4 files
Open
master3329567
4.0 (earliest) Created 25th Jun 2024 at 11:05 by Helena Rasche
Added/updated 4 files
Frozen
4.08a9a246
Creators and Submitter
Views: 197 Downloads: 81
Created: 25th Jun 2024 at 11:05
Last updated: 25th Jun 2024 at 11:05
Tags AttributionsNone
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