TeSS (Training eSupport System)

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- Scientific topic
- Data management172
- Metadata management172
- Research data management (RDM)172
- Comparative transcriptomics148
- Transcriptome148
- Transcriptomics148
- R142
- R program142
- R script142
- FAIR data103
- Findable, accessible, interoperable, reusable data103
- Genome annotation99
- Algorithms97
- Computer programming97
- Data structures97
- Programming languages97
- Software development97
- Software engineering97
- Exomes96
- Genomes96
- Genomics96
- Personal genomics96
- Synthetic genomics96
- Viral genomics96
- Whole genomes96
- MicroRNA sequencing94
- RNA sequencing94
- RNA-Seq94
- RNA-Seq analysis94
- Small RNA sequencing94
- Small RNA-Seq94
- Small-Seq94
- Transcriptome profiling94
- WTSS94
- Whole transcriptome shotgun sequencing94
- miRNA-seq94
- Bayesian methods93
- Biostatistics93
- Descriptive statistics93
- Gaussian processes93
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- Markov processes93
- Multivariate statistics93
- Probabilistic graphical model93
- Probability93
- Statistics93
- Statistics and probability93
- Chromosome walking71
- Clone verification71
- DNA-Seq71
- DNase-Seq71
- High throughput sequencing71
- High-throughput sequencing71
- NGS71
- NGS data analysis71
- Next gen sequencing71
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- Panels71
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- Active learning66
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- Kernel methods66
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- Neural networks66
- Python66
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- Recommender system66
- Reinforcement learning66
- Supervised learning66
- Unsupervised learning66
- py66
- Metagenomics62
- Shotgun metagenomics62
- Bottom-up proteomics61
- Discovery proteomics61
- MS-based targeted proteomics61
- MS-based untargeted proteomics61
- Metaproteomics61
- Peptide identification61
- Protein and peptide identification61
- Proteomics61
- Quantitative proteomics61
- Targeted proteomics61
- Top-down proteomics61
- Bioinformatics49
- Data rendering48
- Data visualisation48
- Single-cell genomics48
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- Antimicrobial stewardship39
- Biological sequences39
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- Operation
- Data handling48
- File handling48
- File processing48
- Processing48
- Report handling48
- Utility operation48
- Data analysis13
- Mathematical modelling11
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- Data extraction10
- Data retrieval10
- Data retrieval (metadata)10
- Metadata retrieval10
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- Data visualisation9
- Molecular visualisation9
- Plotting9
- Rendering9
- Visualisation9
- Database retrieval7
- Query7
- Query and retrieval7
- Database search4
- Normalisation4
- Search4
- Standardisation4
- Standardisation and normalisation4
- Data brokering3
- Data deposition3
- Data deposition brokering3
- Data submission3
- Database deposition3
- Database submission3
- Annotation2
- Data formatting2
- Data management planning2
- Data reformatting2
- Design2
- File format conversion2
- File formatting2
- File reformatting2
- Format conversion2
- RNA-Seq analysis2
- Alignment1
- Alignment construction1
- Alignment generation1
- Allele calling1
- Biological network analysis1
- Biological network modelling1
- Biological network prediction1
- Classification1
- Comparison1
- Exome variant detection1
- Expression analysis1
- Expression data analysis1
- Functional genome annotation1
- Gene expression analysis1
- Gene expression data analysis1
- Gene expression regulation analysis1
- Genome annotation1
- Genome variant detection1
- Germ line variant calling1
- Image analysis1
- Metagenome annotation1
- Metagenomic inference1
- Microarray data analysis1
- Multiple alignment1
- Multiple sequence alignment1
- Mutation detection1
- Network analysis1
- Network comparison1
- Network modelling1
- Network prediction1
- Network simulation1
- Network topology simulation1
- Ontology browsing1
- Ontology visualisation1
- Protein expression analysis1
- Protein secondary structure visualisation1
- Quality control1
- RNA secondary structure visualisation1
- Read pre-processing1
- Sequence classification1
- Sequence read pre-processing1
- Somatic variant calling1
- Structural genome annotation1
- Structure rendering1
- Structure visualisation1
- Validation1
- Variant calling1
- Variant mapping1
- de novo mutation detection1
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- Tool
- Galaxy295
- FastQC34
- SAMtools28
- Bioconductor23
- REDCap20
- BWA19
- MultiQC18
- BEDTools17
- fastp17
- Data Stewardship Wizard16
- scikit-learn15
- SCANPY14
- Cutadapt13
- DeepTools13
- JBrowse13
- QUAST11
- GEMINI10
- RStudio10
- NanoPlot9
- taxonomy_krona_chart9
- BLAST8
- BUSCO8
- RDMkit8
- STAR8
- Trimmomatic8
- kraken28
- FreeBayes7
- Ontology Lookup Service7
- seqtk7
- BCFtools6
- Bandage6
- MaxQuant6
- Open Babel6
- Workflow4Metabolomics6
- ggplot26
- msConvert6
- BamTools5
- Biopython5
- Bowtie 25
- COPASI5
- European Nucleotide Archive (ENA)5
- FASTX-Toolkit5
- Flye5
- Galactic Circos5
- HISAT25
- MSstats5
- MetaPhlAn5
- Minimap25
- RSeQC5
- Unicycler5
- xcms5
- BridgeDb4
- Chipster4
- Diamond4
- HUMAnN24
- KrakenTools4
- MACS4
- MAFFT4
- Merqury4
- MuSiC suite: PoPMuSiC, HoTMuSiC, and SNPMuSiC4
- Newick Utilities4
- The Protein Data Bank (PDB)4
- UniProt4
- annotatemyids4
- gffread4
- mothur4
- snpEff4
- Apollo3
- Bracken3
- BridgeDbR3
- Bwa-mem23
- Cardinal3
- CellProfiler3
- Clustal 1.8 (Clustal W, Clustal X)3
- DISEASES3
- DropletUtils3
- GOseq3
- Galaxy Image Analysis3
- GenomeScope 2.03
- GraPhlAn3
- InterMine3
- InterMineR3
- InterProScan (EBI)3
- MGnify (was EBI Metagenomics)3
- OMERO3
- QualiMap3
- RDKit3
- Salmon3
- SeqCode3
- SortMeRNA3
- Stacks3
- Unipept3
- Zooma3
- bx-python3
- compute_sequence_length3
- export2graphlan3
- gfastats3
- gffcompare3
- humann3
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- Standard database or policy
- FAIRsharing5
- NCBI Gene4
- European Nucleotide Archive3
- RDA DMP Common Standard for Machine-Actionable Data Management Plans3
- DisProt2
- Ensembl2
- Minimum Information about Plant Phenotyping Experiment2
- OBO Foundry2
- Ontology Lookup Service2
- STRING: functional protein association networks2
- Search Tool for Interactions of Chemicals2
- eNanoMapper Ontology2
- Wheat Data Interoperability Guidelines 1
- BRENDA1
- Bioschemas1
- BridgeDb1
- Chemical Entities of Biological Interest1
- Common Workflow Language1
- Crop Ontology1
- FAIR sharing1
- FAIRtracks1
- Gene3D1
- Genomics England | PanelApp1
- HumanMine1
- IUPAC International Chemical Identifier1
- Identifiers.org Registry1
- Integrated resource of protein families, domains and functional sites1
- MDL molfile Format1
- Multi-Crop Passport Descriptors1
- OMOP Common Data Model1
- Observational Medical Outcomes Partnership Standard Vocabulary1
- PRINTS1
- Plant Phenotype Experiment Ontology1
- Resource Identification Portal 1
- SUPERFAMILY1
- Schema.org1
- Simplified Molecular Input Line Entry Specification Format1
- Stress Knowledge Map1
- Structural Classification Of Proteins1
- The FAIR Principles1
- The Human Metabolome Database1
- Wheat Trait Ontology1
- Wikidata1
- data.eNanoMapper.net1
- i2b2-patient_visit_dimensions1
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- Content provider
- GTN679
- Glittr.org663
- European Bioinformatics Institute (EBI)412
- GOBLET108
- SIB Swiss Institute of Bioinformatics92
- ELXIR-UK DaSH70
- Software Carpentry70
- Australian BioCommons55
- DTLS - Dutch Techcentre For Life Sciences41
- de.NBI35
- Bioinformatics and Biomathematics Training Hub34
- Khan Academy Statistics32
- BY-COVID31
- IFB French Institute of Bioinformatics27
- VIB Training26
- Bioconductor24
- Coursera18
- ELIXIR Portugal18
- CINECA PROJECT17
- ELIXIR13
- PerMedCoE12
- NBIS11
- CSC - IT Center for Science10
- eNanoMapper10
- Bioschemas9
- Data Carpentry9
- NanoCommons9
- Barcelona Supercomputing Center (BSC)8
- Department of Bioinformatics - BiGCaT, Maastricht University8
- Genome 3D8
- ELIXIR Estonia7
- ELIXIR Norway7
- InterMine7
- Data Steward team Ghent University6
- ELIXIR Luxembourg6
- ELIXIR-SI eLearning Platform (EeLP)6
- BioData.pt5
- ELIXIR Slovenia5
- LIPID MAPS5
- UNIVERSE-HPC project5
- COG-Train4
- Centre for Genomic Regulation (CRG)4
- Proteomics Academy4
- University of Cambridge Bioinformatics Training4
- Danish National Health Data Science Sandbox3
- ELIXIR: The Czech Republic Node3
- Novo Nordisk Foundation Center for Protein Research3
- VHP4Safety3
- ELIXIR AAI2
- Software Sustainability Institute2
- The Carpentries2
- University of Edinburgh2
- Biomedical Sciences Research Center "Alexander Fleming"1
- Centre for Digital Life Norway1
- Cloud-SPAN1
- EOSC4Cancer1
- ExCALIBUR1
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- proteomicsML1
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- Keyword
- R286
- Python124
- Transcriptomics122
- RNA-seq85
- Genomics80
- Bioinformatics74
- Data management67
- Galaxy Server administration65
- Next generation sequencing65
- Statistics63
- FAIR61
- Machine learning57
- Data science53
- FAIR data53
- Foundations of Data Science50
- data management50
- Single-cell sequencing48
- Reproducibility47
- Proteomics46
- jupyter-notebook46
- Workflows42
- Unix/Linux40
- Data visualization39
- Single Cell37
- microgalaxy36
- General33
- training33
- Variant analysis29
- Version control29
- Development in Galaxy27
- Rare Diseases & Research27
- Contributing to the Galaxy Training Material26
- Data analysis26
- Genome Annotation26
- Metagenomics26
- Assembly25
- RDM25
- Using Galaxy and Managing your Data25
- Epigenetics24
- Ecology22
- Statistics and machine learning22
- data stewardship22
- ansible21
- Containerization20
- Shiny20
- sensitive data19
- Docker19
- FAIR Data, Workflows, and Research19
- Microbiome19
- Nextflow19
- REDCap19
- git-gat19
- interactive-tools19
- life-sciences19
- metadata19
- metagenomics19
- ChIP-seq18
- Cloud computing18
- Programming18
- Metadata17
- Teaching and Hosting Galaxy training17
- Variant Analysis17
- 10x16
- Roslin Institute16
- Shell16
- Climate15
- Metabolomics15
- Sequence analysis15
- fair15
- prokaryote15
- Introduction to Galaxy Analyses14
- Julia14
- gmod14
- jbrowse114
- Data management planning13
- Babraham Institute13
- EeLP13
- Europe PMC13
- Git13
- High performance computing13
- NGS13
- Ontologies13
- eLearning13
- earth-system13
- Clinical data12
- ELIXIR-CONVERGE12
- HPC12
- Literature search12
- Phylogenetics12
- Quarto12
- Spatial transcriptomics12
- Standards12
- bioinformatics12
- covid1912
- cyoa12
- health-informatics12
- paper-replication12
- ATAC-seq11
- CONVERGE11
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- Difficulty level
- Not specified1932
- Beginner777
- Intermediate196
- Advanced37
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- Licence
- License Not Specified1629
- Creative Commons Attribution 4.0 International893
- Creative Commons Attribution Share Alike 4.0 International129
- MIT License81
- Creative Commons Attribution Non Commercial Share Alike 4.0 International33
- Creative Commons Zero v1.0 Universal33
- GNU General Public License v3.0 only32
- Creative Commons Attribution Non Commercial No Derivatives 4.0 International23
- Apache License 2.017
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- Other (Non-Commercial)14
- BSD 3-Clause "New" or "Revised" License12
- Creative Commons Attribution Non Commercial 4.0 International9
- Creative Commons Attribution 1.0 Generic5
- Artistic License 2.02
- Creative Commons Attribution No Derivatives 4.0 International2
- GNU Affero General Public License v3.0 only2
- GNU General Public License v2.0 only2
- Academic Free License v3.01
- Creative Commons Attribution 2.0 Generic1
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- Do What The F*ck You Want To Public License1
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- Target audience
- Students463
- Researchers211
- Biologists, Genomicists, Computer Scientists170
- Post-Doctoral Fellows164
- PhD students139
- Clinicians109
- Galaxy Administrators92
- Graduate students87
- Graduate Students79
- Instructors47
- Novice44
- Life Science Researchers43
- Biologists41
- bioinformaticians35
- Bioinformaticians26
- Intermediate26
- PhD candidate26
- PhD candidates21
- post-docs20
- Scientists19
- Bench biologists18
- Data Managers18
- Academia/ Research Institution17
- Industry17
- Non-Profit Organisation17
- Beginners16
- Data Scientists16
- Trainers16
- life scientists16
- Healthcare15
- beginner bioinformaticians15
- Research Scientists12
- Biomedical Researchers11
- Computational biologists11
- Researcher in life sciences11
- data stewards11
- software developers, bioinformaticians11
- health professionals10
- Master students10
- biocurators10
- Biomedical researchers9
- PhD Students9
- Training Designers9
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- healthcare professionals9
- PhD8
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- modelers7
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- Life scientists6
- Patient Advocates 6
- rare disease patients representatives5
- Chemists5
- Clinical Scientists5
- General Interest5
- Post Docs5
- Researcher5
- Undergraduate students5
- computational scientists5
- data managers5
- plant researchers5
- postgrad5
- project manager5
- Anyone wishing to use bioinformatics resources to find basic information about a virus.4
- Beginner4
- Curators4
- Data stewards4
- Laboratory technicians4
- PI4
- Veterinarians4
- postdocs4
- postdoctoral researchers4
- researchers4
- Biologists with little or no prior computational experience3
- Database users3
- Life scientists with programming skills3
- Ontologists3
- Postgraduate students3
- Technicians3
- data steward / data manager3
- geneticists3
- medical students3
- postdoc3
- programmers3
- research software engineers and researchers writing code3
- software engineers3
- teachers3
- Anyone interested in data standardization and/or the ontology approach (i.e. public, end users).2
- Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities2
- Beginner informatics2
- General Physicians2
- PhD Scholars, Graduates and Post Graduates, Professors, Associate Professors, Assistant Professors, Bio instruments Professionals, Bio-informatics Professionals, Directors, CEO’s of Organizations, Supply Chain companies, Manufacturing Companies, Software development companies, Research Institutes and members2
- Postdocs and Staff members2
- Principal Investigators (PIs)2
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- Author
- Helena Rasche125
- Bérénice Batut93
- SIB Swiss Institute of Bioinformatics73
- Saskia Hiltemann61
- carpentries-incubator46
- Björn Grüning44
- Simon Gladman33
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- The Gulbenkian Training Programme in Bioinformatics27
- bebatut27
- Nicola Soranzo25
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- Saskia Lawson-Tovey24
- The Carpentries23
- Michelle Brazas21
- Yvan Le Bras21
- Fotis E. Psomopoulos20
- NBIS - National Bioinformatics Infrastructure Sweden20
- Wendi Bacon20
- posit-conf-202320
- Egon Willighagen19
- Katarzyna Kamieniecka19
- Subina Mehta19
- Bazante Sanders18
- Krzysztof Poterlowicz18
- Laura Cooper18
- Terri Attwood18
- UC Davis Bioinformatics Core Training Page18
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- Marie Josse17
- Mehmet Tekman17
- Teaching materials at the Harvard Chan Bioinformatics Core17
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- Data Carpentry16
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- Martin Morgan15
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- bioinformatics.ca14
- CRUK CI Bioinformatics Core13
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- Personalized Health Informatics Group12
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- Canadian Bioinformatics Workshops10
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- Martin Čech10
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- Samaha, Georgina (orcid: 0000-0003-0419-1476)10
- Wandrille Duchemin10
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- Anika Erxleben9
- Anup Kumar9
- David Wishart9
- Fred Hutch Data Science Lab9
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- Maria Levchenko8
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- Sara Morsy8
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- Timothy J. Griffin8
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- Contributor
- Saskia Hiltemann509
- Helena Rasche496
- Björn Grüning347
- Bérénice Batut230
- Nicola Soranzo167
- Cristóbal Gallardo103
- Anthony Bretaudeau99
- Niall Beard89
- Martin Čech82
- Nate Coraor71
- Gildas Le Corguillé62
- Marius van den Beek60
- Wendi Bacon59
- William Durand58
- Robert Andrews55
- Simon Gladman54
- Mehmet Tekman46
- carpentries-incubator46
- Lucille Delisle44
- Munazah Andrabi43
- Melanie Föll35
- Yvan Le Bras35
- Beatriz Serrano-Solano30
- Pavankumar Videm29
- SIB Swiss Institute of Bioinformatics28
- Simon Bray28
- Teresa Müller28
- Wolfgang Maier25
- Donny Vrins24
- Subina Mehta24
- Anne Fouilloux23
- Maria Doyle23
- Peter van Heusden23
- Julia Jakiela20
- NBIS - National Bioinformatics Infrastructure Sweden20
- posit-conf-202320
- Bazante Sanders19
- Anton Nekrutenko18
- UC Davis Bioinformatics Core Training Page18
- Anup Kumar17
- Teaching materials at the Harvard Chan Bioinformatics Core17
- posit::conf(2024)17
- Data Carpentry16
- Khaled Jum'ah16
- Deepti Varshney15
- Mélanie Petera14
- bioinformatics.ca14
- CRUK CI Bioinformatics Core13
- Marie Josse13
- Matthias Bernt13
- Pablo Moreno12
- Dave Clements11
- David López11
- Delphine Lariviere11
- Gianmauro Cuccuru11
- Mira Kuntz11
- Stéphanie Robin11
- Canadian Bioinformatics Workshops10
- Instituto Gulbenkian de Ciência10
- John Chilton10
- Marisa Loach10
- The Gulbenkian Training Programme in Bioinformatics10
- @posit-pbc9
- Fred Hutch Data Science Lab9
- Katarzyna Kamieniecka9
- Mallory Freeberg9
- rstudio::conf(2022)9
- Eija Korpelainen8
- Elin Kronander8
- Kaivan Kamali8
- Melissa Burke8
- Paul Zierep8
- Pratik Jagtap8
- Sabine Österle8
- Sundeep Agarwal8
- Tomas Klingström8
- Wolmar Nyberg Åkerström8
- Alexandre Cormier7
- Allyson Lister7
- Anna Syme7
- AstraZeneca7
- Bioinformatics, Rockefeller University7
- Christopher Barnett7
- Daniel Sobral7
- Hans-Rudolf Hotz7
- Markus Englund7
- Mattias Strömberg7
- Niclas Jareborg7
- Sergio Martínez Cuesta7
- Stephan Nylinder7
- Yvonne Kallberg7
- Bert Droesbeke6
- Biocore@CRG6
- Catherine Bromhead6
- Clemens Blank6
- Ekaterina Polkh6
- Enis Afgan6
- Erik Hedman6
- Florian Christoph Sigloch6
- Florian Heyl6
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- Resource type
- e-learning616
- Recorded webinar242
- slides139
- Video116
- Tutorial107
- Training materials51
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- Slidedeck31
- Presentation30
- lessons29
- Documentation28
- hands-on tutorial28
- course materials25
- video24
- Scripts18
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- Handout17
- PDF9
- E-learning8
- Online material5
- Talk5
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- Bioinformatics4
- E-Learning4
- FREE online course4
- podcast4
- Jupyter notebook3
- Life Sciences Literature Database3
- Mock data3
- online course3
- online modules3
- youtube video3
- API reference2
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- Education2
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- scripts2
- slideck/ presentation2
- tutorial2
- tutorials2
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- E-learning + workshop1
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- additional reading1
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- hackathon1
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- implementation guidelines1
- knowledgebase1
- slide deck / presentation1
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- Related resource
- Associated Training Datasets272
- Associated Workflows257
- Jupyter Notebook (with Solutions)42
- Jupyter Notebook (without Solutions)42
- Input datasets32
- Research Data Management in Life Sciences11
- Associated slides9
- The Carpentries7
- Quarto/RMarkdown Notebook6
- Proteomics dataset5
- Sequence analysis dataset5
- Transcriptomics dataset5
- Assembly dataset4
- Variant Analysis dataset4
- Assembly slides3
- DMPonline3
- Data Stewardship Wizard3
- Development in Galaxy slides3
- Slides3
- Workshop recording3
- ChIP-Seq data analysis dataset2
- DisProt2
- Epigenetics dataset2
- Genome Annotation dataset2
- Metagenomics dataset2
- Sequence analysis slides2
- ARROWSMITH1
- Beacon v2: a discovery tool for genomic and pheno-clinical data1
- COBRA Toolbox1
- CanCOGeN1
- Contributing to the Galaxy Training Material slides1
- DMPortal1
- Data Visualisation (theory) 1
- DisGeNET: a discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases1
- EGA Submitter Portal Tutorial1
- ELIXIR's Impact Toolkit1
- ENA1
- Event1
- FAIR for busy biologists1
- FAIR in (biological) practice1
- FAIRplus FAIRification wizard1
- GEEM1
- GPAP: the RD-Connect Genome-Phenome Analysis Platform for diagnosis and gene discovery in rare disease research1
- Galaxy Server administration slides1
- Galaxy project guided tours1
- Genome Annotation slides1
- Genomics England PanelApp1
- GitHub1
- HoloFood Project1
- Introduction to Galaxy Analyses dataset1
- Introduction to Galaxy dataset1
- Introduction to the EGA and sharing sensitive data1
- MGnify1
- MetaboLights1
- MobiDB1
- Next generation biobanking ontology (NGBO)1
- OpenRefine1
- Public Health Alliance for Genomic Epidemiology1
- R basics1
- RDMkit1
- REPET image Docker1
- Ready For BioData Management?1
- Slides | Beacon v2: a discovery tool for genomic and pheno-clinical data1
- Slides | DisGeNET: a discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases1
- Slides | GPAP: the RD-Connect Genome-Phenome Analysis Platform for diagnosis and gene discovery in rare disease research1
- Slides | Introduction to the EGA and sharing sensitive data1
- Statistics dataset1
- Transcriptomics slides1
- User Interface and Features dataset1
- VEIS webinar: The essentials of DUO codes | Presentation1
- VEIS webinar: The essentials of DUO codes | Video1
- Video Walkthrough of the Poster1
- Workshop FAIR & Data stewardship for the 2020 ITN ProEVLifeCycle1
- Workshop FAIR & Data stewardship for the 2021 ITN ProEVLifeCycle1
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Training materials

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Training materials

Introduction to Galaxy Analyses - Introduction to Genomics and Galaxy

Transcriptomics - Visualization of RNA-Seq results with CummeRbund

Proteomics - Peptide and Protein ID using OpenMS tools

Instructor notes

Introduction to Galaxy Analyses - IGV Introduction

Proteomics - Detection and quantitation of N-termini (degradomics) via N-TAILS

Development in Galaxy - Galaxy Code Architecture

Development in Galaxy - Visualizations: generic plugins

Development in Galaxy - BioBlend module, a Python library to use Galaxy API

Development in Galaxy - Galaxy Webhooks