mRNA-Seq BY-COVID Pipeline: Analysis Version 1
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Run on GalaxyAnalyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| factordata | factordata | A two column factor table with (Sample Identifier, Condition) This workflow assumes a 1 factor, 2 level analysis, and was specifically designed around SARS-CoV-2 analysis with two levels, e.g. ``` SampleName Group SRR16683284 COVID SRR16683283 COVID SRR16683271 healthy SRR16683270 healthy ``` |
|
| featureCounts: Counts | featureCounts: Counts | count data collection with two column datasets (gene_id, count) |
|
| featureCounts: Lengths | featureCounts: Lengths | featureCounts Lengths collection |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Column join | toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 |
| 4 | Extract dataset | __EXTRACT_DATASET__ |
| 5 | countdata | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 |
| 6 | annodata | toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1 |
| 7 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 |
| 8 | limma DEG analysis | toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0 |
| 9 | Extract dataset | __EXTRACT_DATASET__ |
| 10 | MINERVA Formatting | Cut1 |
| 11 | Join two Datasets | join1 |
| 12 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.4 |
| 13 | Cut | Cut1 |
| 14 | Unique | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 |
| 15 | Cut | Cut1 |
| 16 | Cut | Cut1 |
| 17 | goseq | toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| count_data | count_data | n/a |
|
| limma_report | limma_report | n/a |
|
| minerva_table | minerva_table | n/a |
|
Version History
Version 1 (earliest) Created 19th Dec 2023 at 10:10 by Helena Rasche
Initial commit
Frozen
Version-1b946ad9
Creators and SubmitterCreators
Additional credit
Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center
Submitter
Views: 5193 Downloads: 962 Runs: 0
Created: 19th Dec 2023 at 10:10
AttributionsNone
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https://orcid.org/0000-0001-9760-8992Failure is not an option.
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Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers.
The goal of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. Ultimately, it will help them gain new insights into how living ...
Teams: ELIXIR Training, FAIR Computational Workflows, EuroScienceGateway, BY-COVID (general), ELIXIR Tools platform, ELIXIR Metabolomics
Web page: https://elixir-europe.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
Team for general BY-COVID contributions
Space: ELIXIR
Public web page: Not specified
canonical record: https://zenodo.org/records/10405036
Source data (GSE182152) was analysed with WFHub:688 to generate these datasets
Creators: Helena Rasche, Iacopo Cristoferi, Marek Ostaszewski, Andrew Stubbs
Submitter: Helena Rasche
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Workflows developed by or used by BY-COVID project.
