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Galaxy Training Network (Project)
Description: The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are...
SEEK ID: https://workflowhub.eu/projects/12
Description: The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are...
SEEK ID: https://workflowhub.eu/projects/12
- Galaxy
- Galaxy Training Network
- Climate - Climate 101
- Trio Analysis
- GTN Training - Antibiotic Resistance Detection
- Genome-wide alternative splicing analysis
- Genome-wide alternative splicing analysis v.2
- StringTie workflow
- Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC
- mRNA-Seq BY-COVID Pipeline
- mRNA-Seq BY-COVID Pipeline: Counts
- mRNA-Seq BY-COVID Pipeline: Analysis
- Ecoregionalization workflow (Part 1)
- Ecoregionalization workflow (Part 2)
- Galaxy Workflow for CNV Detection with CNVkit and Conversion to Beacon JSON Using cnv-vcf2json
- MultiGSEA
- Copy of PeptideDataAnalysis (imported from uploaded file)
- Metagenomics assembly tutorial workflow
- vcf2lineage
- Tutorial workflow
- Subworkflow
- Building an amplicon sequence variant (ASV) table from 16S data using DADA2
- Peptide And Protein ID Tutorial
- WF2_Discovery-Workflow
- Select First N Lines
- Intermine import/export
- ProteinID SG PS Tutorial WF datasetCollection
- Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]
- MaxQuant MSstatsTMT Training
- GTN Training: Workflow Reports
- 'Biomarkers4Paris' Workflow
- Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]
- GTN Training: Workflow Reports - Galaxy 101 For Everyone
- GigaScience-IEDB-PepQuery-Neoantigen
- Proteogenomics 1: Database Creation
- Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]
- GTN_ENA_upload_workflow
- GigaScience_Database_merge_FragPipe_STS26T_demonstration
- ProteoRE ProteomeAnnotation Tutorial (release 2.0)
- Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]
- Circos tutorial
- 'Proteome Annotation'
- Circos: Nature workflow
- GigaScience_PepQuery2_demonstration_STS26T_neoantigen_candidates_workflow
- Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper
- Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]
- Circos for E. Coli
- WF4_Quantitation_Workflow
- DIA_lib_OSW
- Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]
- Pangeo Jupyter Notebook
- Tails Triple Dimethyl OpenMS2.1
- WF3_VERIFICATION_WORKFLOW
- Proteomics: MaxQuant and MSstats for the analysis of label-free data
- CLM-FATES_ ALP1 simulation (5 years)
- Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]
- Proteogenomics 2: Database Search
- GigaScience-RNAseq-Optitype-seq2HLA-to-IEDB-alleles
- Calculating diversity from microbiome taxonomic data
- GTN 'Pangeo 101 for everyone - Xarray'
- WF5_Data_Interpretation_Worklow
- Proteomics: database handling
- WF2_Discovery-Workflow
- Analyse Argo data
- Gigascience_Indels_SAV_non-reference_demonstration_STS26T-Gent_Workflow
- Proteomics: database handling including mycoplasma
- Identification of the micro-organisms in a beer using Nanopore sequencing
- Sentinel5 volcanic data
- Climate 101
- Gigascience_Fusions_demonstration_STS26T-Gent_Workflow
- Metaproteomics_GTN
- Workflow 1: Preprocessing
- Ocean's variables 2.0
- Proteomics: Peptide and Protein ID using OpenMS
- Workflow 3: Functional Information (quick)
- Proteomics: MaxQuant workflow
- Proteomics: Peptide and Protein Quantification via stable istobe labeling
- metaQuantome_datacreation_workflow
- Workflow 2: Community Profile
- Peptide And Protein ID Via OMS Using Two Search Engines
- metaquantome-function-worklow
- PeptideML
- MS Imaging Loading Exploring Data
- Workflow 3: Functional Information
- GigaScience_Peptide_Annotation_demonstration_STS26T_neoantigen_candidates_workflow
- DIA_analysis_MSstats
- metaquantome-taxonomy-workflow
- Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run'
- WF1_Database_Generation_Workflow
- DIA_analysis_MSstats
- DIA_Analysis_OSW
- WF3_VERIFICATION_WORKFLOW
- Training: 16S rRNA Sequencing With Mothur: Main Tutorial
- Main Metatranscriptomics Analysis
- GTN Proteogemics3 Novel Peptide Analysis
- WF4_Quantitation_Workflow
- Query a metaplasmidome database to identify and annotate plasmids in metagenomes
- Taxonomic Profiling and Visualization of Metagenomic Data
- EncyclopeDIA-GTN
- WGS Part In "Analyses Of Metagenomics Data - The Global Picture"
- Training: 16S rRNA Analysis with Nanopore Sequencing Reads
- WF1_Database_Generation_Workflow
- Galaxy Intro Strands
- Amplicon Tutorial
- Copy Of GTN Training - Antibiotic Resistance Detection
- Galaxy Introduction Peaks2Genes - Part 1
- Allele-based Pathogen Identification
- workflow-generate-dataset-for-assembly-tutorial
- Galaxy Intro Short
- WF5_Data_Interpretation_Worklow
- Taxonomy Profiling and Visualization with Krona
- Long non-coding RNAs (lncRNAs) annotation with FEELnc
- scRNA Plant Analysis
- GTN Tutorial: Data manipulation Olympics - all steps and exercises
- Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation
- mrsa AMR gene detection
- GTN Training: Galaxy 101 For Everyone
- CS3_Filter, Plot and Explore Single-cell RNA-seq Data
- CelSeq2: Multi Batch (mm10)
- Nanopore Preprocessing
- Find exons with the highest number of features
- CelSeq2: Single Batch (mm10)
- Gene-based Pathogen Identification
- Filter, Plot and Explore Single-cell RNA-seq Data updated
- Genome Annotation with Prokka
- MuSiC-Deconvolution: Compare
- Capturing mitoflashes
- annotation_helixer
- Filter plot and explore single-cell RNA-seq data with Scanpy (imported from uploaded file)
- scATAC-seq Count Matrix Filtering
- CP_object_tracking_example
- Genome annotation with Maker
- CP_pipeline_IDR_training
- scATAC-seq FASTQ to Count Matrix
- Understanding Barcodes
- feature_extraction
- Genome annotation with Braker3
- Scanpy Parameter Iterator workflow full (imported from URL)
- Single-cell QC with scater
- analyze_screen
- Bacterial Genome Annotation
- GTN_Exemplar_002_TMA_workflow_Feb2025
- GO Enrichment Workflow
- Monocle3 workflow
- Segmentation_Values_Testing
- Comparative gene analysis
- Clustering 3k PBMC with Scanpy
- AnnData object to Monocle input files
- Functional annotation
- Voronoi segmentation
- AnnData to SingleCellExperiment (SCE) conversion
- Trajectory analysis using Monocle3 - full tutorial workflow
- Funannotate
- Image prediction with BioImage.IO model (imported from uploaded file)
- AnnData to Seurat conversion
- 2025_2D_spot_detection
- Inferring Trajectories with Scanpy Tutorial Workflow
- Essential genes detection with Transposon insertion sequencing
- AnnData to Cell Data Set (CDS) conversion
- Workflow constructed from Tutorial 'Introduction to Image Analysis using Galaxy'
- Generating a single cell matrix using Alevin
- Workflow constructed from history 'CRISPR tutorial Kenji'
- EBI SCXA to AnnData (Scanpy) or Seurat Object
- GTN Training: Galaxy 101 For Everyone
- LOCKED | Generating a single cell matrix using Alevin
- RepeatMasker
- Combining datasets after pre-processing
- NGS_tutorial
- GECKO pairwise comparison
- MuSiC-Deconvolution: Data generation | bulk | ESet
- LOCKED | Combining single cell datasets after pre-processing
- Galaxy Intro Strands 2
- CHROMEISTER chromosome comparison
- GTN - Preprocessing of 10X scRNA-seq data
- RaceID Workflow
- MuSiC-Deconvolution: Data generation | sc | matrix + ESet
- Genome annotation with Maker (short)
- Cell Cycle Regression Workflow
- Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2
- MuSiC-Deconvolution: Data generation | sc | metadata
- Music: Pre-grouping cell types
- Apollo Load Test
- Cluster 3k PBMCs with Seurat - Workflow - SCTransform Version
- Pseudobulk with decoupler and edgeR tutorial workflow
- MuSiC: Deconvolution
- Gene Cluster Product Similarity Search
- Tree Building (imported from uploaded file)
- Clustering 3k PBMCs with Seurat - Workflow
- Multisample Batch Correction with SnapATAC2 and Harmony
- CUT&RUN
- Music Stage 1 - Create pseudobulk and actual proportions
- From BAMs to drug resistance prediction with TB-profiler
- NCBI to Anndata
- Workflow Methylation Seq
- Music Stage 4 - Compute metrics
- ATAC-seq GTM
- From VCFs to SNP distance matrix
- Seurat Filter, Plot and Exlore tutorial
- Music Stage 3 - Preprocess Visualisations
- Pathway Analysis
- From Fastqs to VCFs and BAMs
- scRNA Plant Analysis
- Music Stage 2 - Inferring cellular proportions
- Genetic Design (BASIC Assembly)
- Mtb phylogeny
- Assembly polishing - upgraded
- gpu_jupytool
- Assess genome quality - upgraded
- RetroSynthesis
- GC MS using XCMS
- Intro_To_FNN_v1_0_10_0
- Workflow Constructed From History 'imported: testpourGCC'
- Data QC - upgraded
- Finding the Muon Stopping Site: pymuon-suite in Galaxy
- MSI Finding Diff Analytes
- ml_classification
- Trim and filter reads - fastp - upgraded
- Data management in Medicinal Chemistry workflow
- Molecular formula assignment and recalibration with MFAssignR package.
- Classification LSVC
- MSI Workflow: spatial distribution
- Assembly-decontamination-VGP9
- Assembly with Flye - upgraded
- Regression GradientBoosting
- End-to-end EI+ mass spectra prediction workflow using QCxMS
- Unicycler training
- Racon polish with long reads, x4 - upgraded
- Ludwig - Image recognition model - MNIST
- GTN Tutorial: Data manipulation Olympics - all steps and exercises
- Genome Assembly of MRSA using Illumina MiSeq Data
- Simtext training workflow
- Racon polish with Illumina reads (R1 only), x2 - upgraded
- papaa@0.1.9_PI3K_OG_model_tutorial
- Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
- VGP assembly: training workflow
- kmer counting - meryl - upgraded
- Clustering in Machine Learning
- Galaxy Workflow Galaxy Hi C
- Combined workflows for large genome assembly - upgraded
- assembly_with_preprocessing
- Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)
- Ludwig - Image recognition model - MNIST
- GTN - ChIP Seq - Formation Of Super Structures On Xi
- assembly_with_preprocessing_and_sra_download
- Chloroplast-genome-assembly-and-annotation
- fruit_360
- Identification Of The Binding Sites Of The Estrogen Receptor - Qc Mapping
- Identification Of The Binding Sites Of The Estrogen Receptor - Chip Seq
- Genome Assembly using PacBio data
- Intro to Genome Assembly
- Text-Mining Differences in Chinese Newspaper Articles
- Infinium Human Methylation BeadChip
- Retrieve climate data from Copernicus
- Debruijn Graph
- Primer design of a virus family (imported from uploaded file)
- Workflow to detect SNV from Illumina sequenced baculovirus isolates
- MakeAFakeInput
- Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST
- workflow-generate-dataset-for-assembly-tutorial
- pox-virus-tiled-amplicon-ref-masking
- ml_regression
- Metagenomics assembly tutorial workflow
- Training Sanger sequences CHD8
- Trio Analysis Tutorial
- Intro_To_Deep_Learning
- Ecoli Comparison
- Microbial Variant Calling
- GTN - Sequence Analyses - Quality Control (imported from uploaded file)
- Post-assembly workflow
- Simple COVID-19 - PE Variation
- Intro_To_CNN_v1.0.11.0
- Quality and contamination control in bacterial isolate using Illumina MiSeq Data
- GROMACS Training Workflow
- Genome Assembly Quality Control
- TB Variant Analysis v1.0
- Mitogenome-Assembly-VGP0
- CTB Workflow
- Identification and Evolutionary Analysis of Transcription-Associated Proteins
- Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC
- Xarray_Map_Plotting_Workflow
- GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data
- Data management in Medicinal Chemistry workflow
- diploid
- preparing genomic data for phylogeny recostruction (GTN)
- GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file)
- Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring
- Calling variants in non-diploid systems
- Du Novo GTN Tutorial - Variant Calling
- GTN - Sequence Analyses - Mapping (imported from uploaded file)
- Ref Based Rad Seq
- Marine Omics identifying biosynthetic gene clusters
- Du Novo GTN Tutorial - Make Consensus Sequences
- Workflow Constructed From History 'STACKS RAD: Population Genomics With Reference Genome'
- de novo Rad Seq
- GO Enrichment Workflow
- Exome Seq Training Full W Cached Ref
- Sentinel 2 example
- GBIF data Quality check and filtering workflow Feb-2020
- Blockclust 1.1.0 Clustering
- Exome Seq Training Pre-Mapped W Cached Ref
- sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming)
- Checking expected species and contamination in bacterial isolate
- mRNA-Seq BY-COVID Pipeline: Counts
- sRNA Seq Step 2: Salmon And DESeq2
- Workflow Constructed From History 'Heinz Workflow Trial Sep 11'
- Identification of somatic and germline variants from tumor and normal sample pairs tutorial
- BY-COVID: Data Download
- Ecoregionalization workflow
- RNA-RNA interactome data analysis - chira v1.4.3
- Mapping And Molecular Identification Of Phenotype Causing Mutations
- Genetic Map Rad Seq Workflow
- mRNA-Seq BY-COVID Pipeline: Analysis
- De novo transcriptome reconstruction with RNA-Seq
- MD protein-ligand workflow (from PDB structure)
- Species Distribution Modeling With Wallace From GBIF - Training Material
- GTN_differential_isoform_expression
- Workflow constructed from history 'Hsp90-MDAnalysis'
- Champs blocs indicators
- Zauberkugel
- RNA Seq Reads To Counts
- Workflow 'Biodiversity data exploration tuto'
- Analysis using MDAnalysis
- QC report
- Compute and analyze biodiversity metrics with PAMPA toolsuite
- Simple Analysis
- Marine Omics visualisation
- RNA Seq Genes To Pathways (imported from uploaded file)
- NAMD MD From CHARMM GUI
- MD NAMD
- Workflow constructed from history 'Tuto Obitools'
- RNA Seq Counts To Genes
- Tutorial regionalGAM Complete Multispecies
- Phenology "stacked" Visualization Creation
- Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38
- Regional GAM Workflow
- Workflow constructed from history 'Computer assignment RNA seq analysis and visualisation -BMW2 - attempt 3'
- Visualization Of RNA-Seq Results With Volcano Plot
- Abundance Index "stacked" Visualization Creation
- QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows
- NDVI with OpenEO
- DEG Part - Ref Based RNA Seq - Transcriptomics - GTN
- NDVI with OpenEO
- QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN
- trinity NG
- Plant bulk RNA-Seq workflow
- Heatmap2 Workflow
- Workflow Constructed From History 'IWTomics Workflow'
- Machine Learning
- Age Prediction DNA Methylation
- Age Prediction RNA-Seq
- Taxonomic Analysis of eDNA
- Intro_To_RNN_v1_0_10_0
- Galaxy Training Network
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