GTN Bot

Overview
Related items

About GTN Bot:

I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.

SEEK ID: https://workflowhub.eu/people/731

Location: Not specified

ORCID: Not specified

Joined: 23rd Apr 2024

Expertise: AI, Workflows

Tools: Python

Their tags

10X Arabidopsis Asaim Assembly Big-data bioimaging Braker3 BUSCO cancer CellProfiler Cheminformatics Chinese-language Chowell_train_test Classification Climate Clustering Comparison Computational-chemistry Contributing copernicus Cut&run Deeplearning Diff Digitalhumanities Earth-system Ecology epigenetics evolution Exposomics Expospomics Fnn Formulaassignment Fungi Galaxy Galaxy-interface GC-MS genome-annotation Genomeannotation Genomics Geosciences GTN hCNV Helixer hla Humanities IDR Iedb imageanaylsis Imagerecognition imaging Introduction Introductions Iwtomics Jbrowse Lg-wf Llr6_model Logistic_regression_model Loris Lotus2 Ludwig Marineomics Metabolomics Metagenomics Metaplasmidome microbiome Microgalaxy MIRACUM Mirna Mito-flash Mitochondrion_tracking Ml Mnist Moleculardynamics Multi-omics Name:bacsnp Name:baculoviridae Name:baculovirus Name:by-covid Name:circos Name:clinicalmp name:Collection Name:data-management Name:deconv-eval Name:deconvolution name:ERGA Name:gtn Name:iwc Name:microgalaxy Name:naldv Name:nanopore Name:neoantigen Name:pathogfair Name:scrna-seq Name:sequenceanalysis Name:seurat name:single-cell Name:single_cell Name:singlecell name:training Name:trajectory_analysis Name:transcriptomics Name:viz Noiseestimation Ocean pangeo pathogen Proteomics Pseudobulk Published Pubmed Pubtator QCxMS Recalibration referencegenome Regression Reviewed rna scATAC-seq Segmentation Sempi3 Sequence-analysis single-cell Smfish Statistics synthetic-biology Text Text-mining Text_mining Transcriptomics tuberculosis variant-analysis vgp VGP_curated Visualisation visualization Voronoi

Related items

Advanced Spaces list for this Person with search and filtering

Galaxy

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

Web page: https://galaxyproject.org/

Advanced Teams list for this Person with search and filtering

Galaxy Training Network

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!

Space: Galaxy

Public web page: https://training.galaxyproject.org

Start date: 1st Sep 2017

Organisms: Homo sapiens, SARS-CoV-2

Advanced Organizations list for this Person with search and filtering

Galaxy

Country: Not specified

City: Not specified

Web page: Not specified

Showing 20 out of a possible 345 Workflows Advanced Workflows list for this Person with search and filtering

Workflow 3: Functional Information (quick)

Galaxy Training Network

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Associated Tutorial

This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN

Features

Includes Galaxy Workflow Tests ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 10:53, Last updated: 14th Jul 2025 at 14:14

GigaScience-RNAseq-Optitype-seq2HLA-to-IEDB-alleles

Galaxy Training Network

Prediction of HLA binding for verified candidates

Associated Tutorial

This workflows is part of the tutorial Neoantigen 5a: Predicting HLA Binding, available in the GTN

Features

Includes a Galaxy Workflow Report

Thanks to...

...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 7th Jul 2025 at 14:16

GigaScience_Database_merge_FragPipe_STS26T_demonstration

Galaxy Training Network

Merging Fusion and non-normal databases + Discovery peptidomics using FragPipe

Associated Tutorial

This workflows is part of the tutorial Neoantigen 2: Database merge and FragPipe discovery, available in the GTN

Features

Includes a Galaxy Workflow Report ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 7th Jul 2025 at 14:16

Gigascience_Fusions_demonstration_STS26T-Gent_Workflow

Galaxy Training Network

Create a protein Fusion database through the Arriba workflow

Associated Tutorial

This workflows is part of the tutorial Neoantigen 1a: Fusion-Database-Generation, available in the GTN

Features

Includes a Galaxy Workflow Report ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 7th Jul 2025 at 14:15

GigaScience_PepQuery2_demonstration_STS26T_neoantigen_candidates_workflow

Galaxy Training Network

Validate the NeoAntigen Candidates from FragPipe discovery through the PepQuery Novel search

Associated Tutorial

This workflows is part of the tutorial Neoantigen 3: PepQuery2 Verification, available in the GTN

Features

Includes a Galaxy Workflow Report ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 7th Jul 2025 at 14:15

GigaScience_Peptide_Annotation_demonstration_STS26T_neoantigen_candidates_workflow

Galaxy Training Network

Annotating the novel peptides

Associated Tutorial

This workflows is part of the tutorial Neoantigen 4: Variant Annotation, available in the GTN

Features

Includes a Galaxy Workflow Report

Thanks to...

Workflow Author(s): GalaxyP ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 7th Jul 2025 at 14:15

GigaScience-IEDB-PepQuery-Neoantigen

Galaxy Training Network

Predict binding using IEDB and check novelty peptides with PepQuery

Associated Tutorial

This workflows is part of the tutorial Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides, available in the GTN

Features

Includes a Galaxy Workflow Report ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 7th Jul 2025 at 14:15

Gigascience_Indels_SAV_non-reference_demonstration_STS26T-Gent_Workflow

Galaxy Training Network

Generating non-reference protein database for FragPipe discovery

Associated Tutorial

This workflows is part of the tutorial Neoantigen 1b: Non-Reference-Database-Generation, available in the GTN

Features

Includes a Galaxy Workflow Report ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 7th Jul 2025 at 14:15

Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation

Galaxy Training Network

Pathogens of all samples report generation and visualization

Associated Tutorial

This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN

Features

Includes a [Galaxy Workflow ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 10:55, Last updated: 7th Jul 2025 at 14:14

Nanopore Preprocessing

Galaxy Training Network

Microbiome - QC and Contamination Filtering

Associated Tutorial

This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN

Features

Includes Galaxy Workflow Tests ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 10:55, Last updated: 7th Jul 2025 at 14:14

Building an amplicon sequence variant (ASV) table from 16S data using DADA2

Galaxy Training Network

Building an amplicon sequence variant (ASV) table from 16S data using DADA2

Associated Tutorial

This workflows is part of the tutorial Building an amplicon sequence variant (ASV) table from 16S data using DADA2, available in the GTN

Features

Includes Galaxy Workflow Tests ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 10:51, Last updated: 7th Jul 2025 at 14:14

Comparison of two annotation tools: Helixer and Braker3

Galaxy Training Network

The idea of this workflow is to compare annotation with two annotation tools that differ in their approach and operation.

Associated Tutorial

This workflows is part of the tutorial Comparison of two annotation tools - Helixer and Braker3, available in the GTN

Features

Includes [Galaxy Workflow ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 23rd Jun 2025 at 14:13

Metatranscriptomics analysis using microbiome RNA-seq data

Galaxy Training Network

Metatranscriptomics analysis using microbiome RNA-seq data

Associated Tutorial

This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data, available in the GTN

Features

Includes Galaxy Workflow Tests
Includes ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 10:54, Last updated: 23rd Jun 2025 at 14:13

Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 2: Community profile

Galaxy Training Network

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Associated Tutorial

This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN

Features

Includes Galaxy Workflow Tests ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 10:53, Last updated: 23rd Jun 2025 at 14:13

Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 1: Preprocessing

Galaxy Training Network

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Associated Tutorial

This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN

Features

Includes Galaxy Workflow Tests ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 10:53, Last updated: 23rd Jun 2025 at 14:13

Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 3: Functional Information

Galaxy Training Network

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Associated Tutorial

This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN

Features

Includes Galaxy Workflow Tests ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 10:54, Last updated: 23rd Jun 2025 at 14:13

Assembly of metagenomic sequencing data

Galaxy Training Network

Assembly of metagenomic sequencing data

Associated Tutorial

This workflows is part of the tutorial Assembly of metagenomic sequencing data, available in the GTN

Features

Includes Galaxy Workflow Tests
Includes a [Galaxy Workflow ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 10:51, Last updated: 16th Jun 2025 at 14:13

Intro_To_RNN_v1_0_10_0

Galaxy Training Network

Associated Tutorial

This workflows is part of the tutorial Deep Learning (Part 2) - Recurrent neural networks (RNN), available in the GTN

Features

Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Kaivan Kamali

Tutorial Author(s): [Kaivan ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 14:16

Taxonomic Analysis of eDNA

Galaxy Training Network

Final output is a table of Taxa and how many sequences aligned with them. This table can be used to then visualize via a pie chart.

Associated Tutorial

This workflows is part of the tutorial Taxonomic Analysis of eDNA, available in the GTN

Features

Includes a Galaxy Workflow Report ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 14:16

Age Prediction RNA-Seq

Galaxy Training Network

Age prediction using machine learning

Associated Tutorial

This workflows is part of the tutorial Age prediction using machine learning, available in the GTN

Thanks to...

Tutorial Author(s): Ekaterina Polkh, [Anup ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Created: 2nd Jun 2025 at 14:16

View all 345 Workflows