Materials - TeSS (Training eSupport System)

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- Data management234
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- Genome annotation230
- Exomes208
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- Genomics208
- Personal genomics208
- Synthetic genomics208
- Viral genomics208
- Whole genomes208
- Comparative transcriptomics191
- Transcriptome191
- Transcriptomics191
- MicroRNA sequencing173
- RNA sequencing173
- RNA-Seq173
- RNA-Seq analysis173
- Small RNA sequencing173
- Small RNA-Seq173
- Small-Seq173
- Transcriptome profiling173
- WTSS173
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- FAIR data164
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- R153
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- Statistics and probability148
- Algorithms129
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- High-throughput sequencing116
- Chromosome walking115
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- DNA-Seq115
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- Python78
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- py78
- Bottom-up proteomics75
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- Proteomics75
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- Biodiversity69
- Single-cell genomics62
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- Antimicrobial stewardship56
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- Operation
- Data handling48
- File handling48
- File processing48
- Processing48
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- Utility operation48
- Data visualisation15
- Molecular visualisation15
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- Visualisation15
- Data analysis13
- Annotation11
- Mathematical modelling11
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- Data extraction10
- Data retrieval10
- Data retrieval (metadata)10
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- Database retrieval8
- Query8
- Query and retrieval8
- Quality control5
- Validation5
- Allele calling4
- Data management planning4
- Database search4
- Exome variant detection4
- Functional enrichment analysis4
- GSEA4
- Gene set analysis4
- Gene-set enrichment analysis4
- Gene-set over-represenation analysis4
- Genome variant detection4
- Germ line variant calling4
- Methylation analysis4
- Methylation profile analysis4
- Mutation detection4
- Normalisation4
- Search4
- Somatic variant calling4
- Standardisation4
- Standardisation and normalisation4
- Variant calling4
- Variant mapping4
- de novo mutation detection4
- Data brokering3
- Data deposition3
- Data deposition brokering3
- Data submission3
- Database deposition3
- Database submission3
- Data formatting2
- Data reformatting2
- Design2
- File format conversion2
- File formatting2
- File reformatting2
- Format conversion2
- Peptide database search2
- Peptide identification2
- Peptide-spectrum-matching2
- RNA-Seq analysis2
- Alignment1
- Alignment construction1
- Alignment generation1
- Biological network analysis1
- Biological network modelling1
- Biological network prediction1
- Classification1
- Comparison1
- Data filtering1
- Expression analysis1
- Expression data analysis1
- Functional genome annotation1
- Gene expression analysis1
- Gene expression data analysis1
- Gene expression regulation analysis1
- Genome annotation1
- Image analysis1
- Metagenome annotation1
- Metagenomic inference1
- Microarray data analysis1
- Multiple alignment1
- Multiple sequence alignment1
- Network analysis1
- Network comparison1
- Network modelling1
- Network prediction1
- Network simulation1
- Network topology simulation1
- Ontology browsing1
- Ontology visualisation1
- Protein expression analysis1
- Protein secondary structure visualisation1
- RNA secondary structure visualisation1
- Read pre-processing1
- Sequence classification1
- Sequence filtering1
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- Tool
- Galaxy364
- Bioconductor242
- FastQC36
- SAMtools27
- MultiQC26
- BWA21
- REDCap20
- Data Stewardship Wizard19
- BEDTools17
- fastp16
- scikit-learn16
- JBrowse15
- SCANPY15
- Falco14
- Cutadapt13
- DeepTools13
- ggplot213
- BLAST12
- QUAST12
- BUSCO11
- RStudio11
- STAR11
- GEMINI10
- Galaxy Image Analysis10
- scikit-image10
- taxonomy_krona_chart10
- FreeBayes9
- NanoPlot9
- RDMkit9
- Trimmomatic9
- Bandage8
- FASTX-Toolkit8
- BCFtools7
- BamTools7
- Biopython7
- HISAT27
- Trim Galore7
- msConvert7
- seqtk7
- Flye6
- MAFFT6
- MaxQuant6
- Minimap26
- Ontology Lookup Service6
- Open Babel6
- Unicycler6
- Workflow4Metabolomics6
- gffread6
- BridgeDb5
- COPASI5
- DESeq25
- European Nucleotide Archive (ENA)5
- Galactic Circos5
- MetaPhlAn5
- MuSiC suite: PoPMuSiC, HoTMuSiC, and SNPMuSiC5
- RSeQC5
- SRA Software Toolkit5
- Salmon5
- StringTie5
- anndata5
- annotatemyids5
- compute_sequence_length5
- gffcompare5
- kraken25
- xcms5
- Bowtie 24
- Bwa-mem24
- CellProfiler4
- Chipster4
- Diamond4
- GOseq4
- KrakenTools4
- MACS4
- MSstats4
- Merqury4
- Newick Utilities4
- QualiMap4
- The Protein Data Bank (PDB)4
- UniProt4
- bx-python4
- mothur4
- snpEff4
- Apollo3
- Bakta3
- Bracken3
- BridgeDbR3
- Cardinal3
- Clustal 1.8 (Clustal W, Clustal X)3
- DISEASES3
- DropletUtils3
- FastTree3
- GenomeScope 2.03
- GraPhlAn3
- InterMine3
- InterMineR3
- InterProScan (EBI)3
- MGnify (was EBI Metagenomics)3
- OMArk3
- OMERO3
- R3
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- Standard database or policy
- FAIRsharing5
- NCBI Gene4
- Bioconductor3
- Ensembl3
- European Nucleotide Archive3
- RDA DMP Common Standard for Machine-Actionable Data Management Plans3
- Common Workflow Language2
- DisProt2
- Minimum Information about Plant Phenotyping Experiment2
- OBO Foundry2
- Ontology Lookup Service2
- PRoteomics IDEntifications database2
- STRING: functional protein association networks2
- Search Tool for Interactions of Chemicals2
- The European Genome-phenome Archive2
- The Observational Medical Outcomes Partnership Common Data Model2
- eNanoMapper Ontology2
- Wheat Data Interoperability Guidelines 1
- BRENDA1
- BcForms Grammar1
- Bioschemas1
- BpForms Grammar1
- BridgeDb1
- Cellosaurus1
- Chemical Entities of Biological Interest1
- Crop Ontology1
- Datanator1
- FAIR sharing1
- FAIRtracks1
- Gene3D1
- Genomics England | PanelApp1
- HumanMine1
- IUPAC International Chemical Identifier1
- Identifiers.org Registry1
- Integrated resource of protein families, domains and functional sites1
- Investigation Study Assay JSON1
- Investigation Study Assay Tabular1
- MDL molfile Format1
- ModelArchive1
- Multi-Crop Passport Descriptors1
- ObjTables1
- Observational Medical Outcomes Partnership Standard Vocabulary1
- PRINTS1
- Plant Phenotype Experiment Ontology1
- Research Object Crate1
- 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
- UniProt Knowledgebase1
- Wheat Trait Ontology1
- Wikidata1
- WorkflowHub1
- Worldwide Protein Data Bank1
- Zenodo 1
- data.eNanoMapper.net1
- i2b2-patient_visit_dimensions1
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- Content provider
- GTN832
- Glittr.org831
- European Bioinformatics Institute (EBI)488
- Bioconductor242
- IFB French Institute of Bioinformatics149
- ERGA Knowledge Hub128
- SIB Swiss Institute of Bioinformatics113
- GOBLET110
- Australian BioCommons88
- Bioinformatics Visualization72
- ELXIR-UK DaSH70
- Software Carpentry70
- Bioinformatics and Biomathematics Training Hub62
- NGS Registry60
- DTLS - Dutch Techcentre For Life Sciences41
- VIB Training & Conferences38
- de.NBI35
- Data Carpentry34
- Khan Academy Statistics32
- BY-COVID31
- VIB Bioinformatics Core29
- Canadian Bioinformatics Workshops26
- ELIXIR24
- Coding for Reproducible Research (CfRR)19
- Coursera19
- VBCF BioComp19
- ELIXIR Portugal18
- CINECA PROJECT17
- CSC - IT Center for Science12
- ELIXIR Estonia12
- PerMedCoE12
- NBIS11
- ELIXIR Norway10
- VHP4Safety10
- eNanoMapper10
- Bioschemas9
- EMBL-ABR9
- NanoCommons9
- Barcelona Supercomputing Center (BSC)8
- Department of Bioinformatics - BiGCaT, Maastricht University8
- Genome 3D8
- InterMine8
- Centre for Genomic Regulation (CRG)7
- BioData.pt6
- Data Steward team Ghent University6
- ELIXIR Luxembourg6
- ELIXIR-SI eLearning Platform (EeLP)6
- ELIXIR: The Czech Republic Node6
- Danish National Health Data Science Sandbox5
- ELIXIR Slovenia5
- LIPID MAPS5
- UNIVERSE-HPC project5
- COG-Train4
- Proteomics Academy4
- University of Cambridge Bioinformatics Training4
- ELIXIR AAI3
- Novo Nordisk Foundation Center for Protein Research3
- Pattern Institute3
- University of Edinburgh3
- DeiC – Danish e-Infrastructure Cooperation2
- SciLifeLab2
- Software Sustainability Institute2
- The Carpentries2
- Biomedical Sciences Research Center "Alexander Fleming"1
- CNAG-CRG1
- Centre for Digital Life Norway1
- Cloud-SPAN1
- EOSC4Cancer1
- ExCALIBUR1
- FAIRsharing1
- Fraunhofer FIT1
- Future Learn1
- Health-RI1
- NYU Langone Health1
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- Seqera1
- UCLouvain Bioinformatics Platform1
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- Keyword
- R331
- Genomics168
- Transcriptomics160
- Python149
- RNA-seq127
- Next generation sequencing119
- Data management104
- Bioinformatics98
- Statistics80
- FAIR data77
- FAIR69
- Galaxy Server administration68
- Machine learning68
- Reproducibility68
- Data science67
- Single-cell sequencing61
- Unix/Linux61
- Proteomics56
- jupyter-notebook55
- Workflows54
- Data visualization51
- Version control51
- Foundations of Data Science50
- Variant analysis50
- data management48
- biodiversity47
- metagenomics47
- Development in Galaxy45
- Statistics and machine learning45
- Genome assembly43
- Galaxy41
- Single Cell41
- microgalaxy41
- training39
- Metagenomics38
- General36
- Genome annotation36
- Rare Diseases & Research36
- FAIR Data, Workflows, and Research33
- QC33
- Microbiome32
- Nextflow32
- Genome Annotation31
- Ecology30
- programming30
- Assembly28
- FAIR principles28
- Genome28
- Metadata28
- Molecular28
- Alignment27
- Contributing to the Galaxy Training Material27
- Data analysis27
- Phylogenetics27
- Using Galaxy and Managing your Data27
- biohackaton 201827
- Epigenetics26
- Long read sequencing26
- RDM26
- bioinformatics26
- Docker25
- Data reuse24
- Annotation23
- Containerization23
- data stewardship23
- ChIP-seq22
- High performance computing22
- Metabolomics22
- Microbiology22
- Shiny22
- NGS21
- Open Science21
- RNA-Seq21
- Spatial transcriptomics21
- ansible21
- metadata21
- reproducible research21
- BAM20
- FASTQ20
- Research Data Management20
- life-sciences20
- sensitive data19
- CfRR19
- Cloud computing19
- Differential-expression19
- FAIR Data19
- Imaging19
- Pre-processing19
- REDCap19
- Sequence analysis19
- git-gat19
- scientific computing19
- Artificial intelligence18
- Comparative genomics18
- Data sharing18
- Programming18
- Variant Analysis18
- interactive-tools18
- transcriptomics18
- work-in-progress18
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- Not specified3040
- Beginner954
- Intermediate283
- Advanced50
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- License Not Specified2521
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- Creative Commons Attribution Share Alike 4.0 International144
- MIT License130
- GNU General Public License v3.0 only50
- Creative Commons Attribution Non Commercial No Derivatives 4.0 International45
- Creative Commons Zero v1.0 Universal43
- Creative Commons Attribution Non Commercial Share Alike 4.0 International41
- Other (Not Open)24
- Apache License 2.017
- Other (Non-Commercial)15
- BSD 3-Clause "New" or "Revised" License14
- Creative Commons Attribution Non Commercial 4.0 International12
- Other (Attribution)6
- Creative Commons Attribution 1.0 Generic5
- CeCILL Free Software License Agreement v2.13
- Creative Commons Attribution No Derivatives 4.0 International3
- Other (Open)3
- Artistic License 2.02
- 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
- Creative Commons Attribution No Derivatives 2.0 Generic1
- Creative Commons Attribution Non Commercial 2.0 Generic1
- Do What The F*ck You Want To Public License1
- Open Data Commons Attribution License v1.01
- The Unlicense1
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- Target audience
- Students573
- Researchers240
- PhD students184
- Biologists, Genomicists, Computer Scientists170
- Post-Doctoral Fellows164
- Clinicians128
- Galaxy Administrators113
- Graduate students88
- Graduate Students82
- Life Science Researchers78
- Biologists55
- Instructors52
- post-docs47
- Novice44
- bioinformaticians42
- Bioinformaticians33
- Intermediate26
- PhD candidate26
- Scientific community26
- beginner bioinformaticians25
- PhD candidates23
- Data stewards22
- Scientists22
- Bench biologists19
- Data Managers19
- Academia/ Research Institution17
- Industry17
- Non-Profit Organisation17
- Beginners16
- Data Scientist16
- Data Scientists16
- Data managers16
- Trainers16
- life scientists16
- Healthcare15
- PhD Students15
- health professionals13
- Researcher in life sciences13
- data stewards13
- Computational biologists12
- Master students12
- Research Scientists12
- healthcare professionals12
- software developers, bioinformaticians12
- Biomedical Researchers11
- biocurators11
- Researcher10
- Biomedical researchers9
- Life scientists9
- Training Designers9
- Training instructors9
- biologists9
- Health Care Professionals8
- Patient Advocates 8
- PhD8
- Post Docs8
- modelers8
- rare disease patients representatives7
- Beginner7
- Bioinformatician7
- Life Scientists7
- Life scientists with programming skills7
- Clinical Scientists6
- computational scientists6
- data managers6
- plant researchers6
- Chemists5
- General Interest5
- PI5
- Undergraduate students5
- genomics researchers5
- postdocs5
- postgrad5
- project manager5
- Anyone wishing to use bioinformatics resources to find basic information about a virus.4
- Biologists with little or no prior computational experience4
- Curators4
- Laboratory technicians4
- 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 members4
- Postgraduate students4
- Veterinarians4
- postdoctoral researchers4
- researchers4
- systems biologists4
- Bioinformatician, Bioanalysts3
- Data Steward3
- Database users3
- General Physicians3
- Ontologists3
- Policy makers3
- Researchers and bioinformaticians in other projects interested in depositiong data at the EGA3
- Technicians3
- data steward / data manager3
- geneticists3
- life science researchers3
- medical students3
- postdoc3
- programmers3
- research software engineers and researchers writing code3
- software engineers3
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- Author
- Helena Rasche127
- Bérénice Batut111
- SIB Swiss Institute of Bioinformatics107
- Martin Morgan97
- Saskia Hiltemann66
- The Carpentries Incubator52
- Björn Grüning50
- Simon Gladman37
- The Gulbenkian Training Programme in Bioinformatics36
- bioinformatics.ca35
- bebatut32
- bgruening32
- Anthony Bretaudeau28
- Anton Nekrutenko28
- Yvan Le Bras28
- Nate Coraor27
- Subina Mehta27
- Donat Agosti25
- John Chilton25
- Julia Giora25
- Nicola Soranzo25
- Plazi Verein25
- Teaching materials at the Harvard Chan Bioinformatics Core25
- Saskia Lawson-Tovey24
- The Carpentries24
- Egon Willighagen22
- Fotis E. Psomopoulos21
- Michelle Brazas21
- NBIS - National Bioinformatics Infrastructure Sweden20
- posit-conf-202320
- Anne Fouilloux19
- Coding for Reproducible Research Initiative19
- Marie Josse19
- Wendi Bacon19
- Bazante Sanders18
- Katarzyna Kamieniecka18
- Krzysztof Poterlowicz18
- Laura Cooper18
- Terri Attwood18
- UC Davis Bioinformatics Core Training Page18
- András Aszódi17
- Data Carpentry17
- Mehmet Tekman17
- posit::conf(2024)17
- shiltemann17
- Paul Zierep16
- Wandrille Duchemin16
- Cristóbal Gallardo15
- Samaha, Georgina15
- Sergio Martínez Cuesta15
- Alexander Botzki14
- Julia Jakiela14
- Maria Doyle14
- Mijke Jetten14
- Pratik Jagtap14
- nekrut14
- CRUK CI Bioinformatics Core13
- Dave Clements13
- Delphine Lariviere13
- Donny Vrins13
- James Johnson13
- Katherine Do13
- Monique Zahn13
- Wolfgang Maier13
- Andrew Mason12
- Celia van Gelder12
- Jenny Drnevich @jenny12
- Marius van den Beek12
- Melanie Föll12
- Patricia Palagi12
- Personalized Health Informatics Group12
- Simon Andrews12
- Simon Bray12
- Anup Kumar11
- Khaled Jum'ah11
- Mathieu Bourgey11
- Pavankumar Videm11
- Various11
- Allegra Via10
- Canadian Bioinformatics Workshops10
- Daniel Blankenberg10
- Eija Korpelainen10
- Fred Hutch Data Science Lab10
- Martin Čech10
- Paul Yorke10
- Anika Erxleben9
- David Wishart9
- ELIXIR Estonia9
- Jared Simpson9
- Lucille Delisle9
- Praveen Kumar9
- allegra.via Via9
- rstudio::conf(2022)9
- Anne Pajon8
- Avans Hogeschool8
- Bastian Schiffthaler @bastian8
- Boris Steipe8
- Diana Pilvar8
- Emma Leith8
- Geert van Geest8
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- Contributor
- Saskia Hiltemann594
- Helena Rasche501
- Björn Grüning420
- Bérénice Batut263
- Nicola Soranzo179
- Martin Čech128
- Anthony Bretaudeau107
- Cristóbal Gallardo104
- Niall Beard90
- Toby Hodges79
- Wendi Bacon77
- Nate Coraor70
- François Michonneau68
- Armin Dadras64
- Gildas Le Corguillé63
- Erin Becker62
- Marius van den Beek60
- William Durand59
- Zhian N. Kamvar58
- Mine Cetinkaya-Rundel56
- Robert Andrews55
- Simon Gladman54
- Katrin Leinweber53
- Raniere Silva53
- Tracy Teal53
- W. Trevor King51
- Andy Boughton50
- maneesha50
- Beatriz Serrano-Solano49
- Katie Anne Mills48
- Teresa Müller48
- Maxim Belkin47
- Lucille Delisle46
- Mehmet Tekman46
- Yvan Le Bras45
- Canadian Bioinformatics Workshops43
- David Pérez-Suárez43
- Gabriel A. Devenyi43
- Munazah Andrabi43
- Abby Cabunoc Mayes42
- EvanWill42
- Ian Lee42
- Jon Pipitone42
- Jonah Duckles42
- Michael Hansen42
- Piotr Banaszkiewicz42
- Brandon Curtis41
- David Mawdsley41
- Greg Wilson41
- Jemma Stachelek41
- Remi Rampin41
- Allen Lee40
- Andrew Sanchez40
- Michael R. Crusoe40
- Pavankumar Videm40
- Jeff Oliver39
- Joel Nothman39
- Nick Young39
- naught10139
- James Allen38
- Rémi Emonet38
- William L. Close38
- Rayna M Harris37
- Marie Josse36
- Wolfgang Maier36
- Melanie Föll35
- Sarah Brown35
- Gerard Capes33
- Anup Kumar32
- Maria Doyle32
- trk31
- Ana Conrado29
- K.E. Koziar29
- Stephan Druskat29
- Simon Bray28
- Subina Mehta28
- Alex Whan27
- Renato Alves27
- Christina K.26
- Paula Andrea Martinez26
- Anne Fouilloux25
- Michael Joseph25
- Anthony Gitter24
- Donny Vrins24
- João Rodrigues24
- Geert van Geest23
- Peter van Heusden23
- Julia Jakiela21
- Sarah Stevens21
- Wolmar Nyberg Åkerström21
- actions-user21
- Henry Schreiner20
- Hilmar Lapp20
- Robert Davey20
- Bazante Sanders19
- Leonid Kostrykin19
- The Gulbenkian Training Programme in Bioinformatics19
- Anton Nekrutenko18
- Elin Kronander18
- Niclas Jareborg18
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- Resource type
- e-learning739
- Recorded webinar301
- Video196
- slides191
- Tutorial133
- Training materials76
- Presentation66
- Webinar62
- Course materials61
- Talk53
- lessons53
- Slides51
- tutorial50
- hands-on tutorial38
- video38
- Slidedeck31
- Documentation30
- course materials29
- exercise26
- Scripts20
- Exercise18
- Handout17
- Lecture16
- Poster16
- PDF14
- Slideshow14
- E-learning9
- E-Learning8
- Jupyter notebook7
- Series of videos6
- Online material6
- Bioinformatics5
- Coding5
- FREE online course5
- online modules5
- tutorials5
- youtube video5
- examples4
- online course4
- podcast4
- Book3
- Computational Biology3
- Computer Science3
- Computer Software3
- Data Science3
- Education3
- How-to guide3
- Learning pathway3
- Life Sciences Literature Database3
- Mock data3
- Programming3
- online tutorial3
- scripts3
- slideck/ presentation3
- API reference2
- Installation instructions2
- Manual2
- Open educational resource2
- Series of videos2
- Vignette2
- case studies2
- e-Learning2
- educational materials2
- handbook2
- knowledgebase2
- presentation2
- workflow2
- Blog post1
- Carpentries style curriculum1
- E-learning + workshop1
- Educational Resource1
- Jupyter notebooks1
- Life Science Literature Database1
- Machine Learning1
- Metadata Registry1
- Notes1
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- R Shiny application1
- Recording1
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- Toolkit1
- Training materials with mock data1
- Transcriptomics1
- ViralZone1
- Workshop1
- additional reading1
- didactic activities1
- hackathon1
- implementation guidelines1
- slide deck / presentation1
- slides / presentation1
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- Related resource
- Associated Training Datasets326
- Associated Workflows305
- Jupyter Notebook (with Solutions)53
- Jupyter Notebook (without Solutions)53
- Input datasets34
- Research Data Management in Life Sciences11
- Associated slides9
- The Carpentries7
- Development in Galaxy slides6
- Quarto/RMarkdown Notebook6
- Proteomics dataset5
- Sequence analysis dataset5
- Transcriptomics dataset5
- Assembly dataset4
- Slides4
- Variant Analysis dataset4
- Assembly slides3
- DMPonline3
- Data Stewardship Wizard3
- Workshop recording3
- ChIP-Seq data analysis dataset2
- DisProt2
- Epigenetics dataset2
- Galaxy Server administration slides2
- Genome Annotation dataset2
- Metagenomics dataset2
- OpenCloning2
- Sequence analysis slides2
- pydna2
- ARROWSMITH1
- Beacon v2: a discovery tool for genomic and pheno-clinical data1
- COBRA Toolbox1
- CanCOGeN1
- Chipster1
- 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 project guided tours1
- Genome Annotation slides1
- Genomics England PanelApp1
- GitHub1
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