Materials - PaN Training

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- Operation
- Data handling46
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- Data visualisation15
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- Quality control5
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- Allele calling4
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- 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 management planning3
- 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
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- Classification1
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- Genome annotation1
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- Tool
- Galaxy371
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- FastQC36
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- BWA21
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- BEDTools17
- fastp16
- scikit-learn16
- JBrowse15
- SCANPY15
- Falco14
- ggplot214
- DeepTools13
- BLAST12
- Cutadapt12
- QUAST12
- BUSCO11
- Galaxy Image Analysis11
- RStudio11
- STAR11
- GEMINI10
- scikit-image10
- taxonomy_krona_chart10
- FreeBayes9
- NanoPlot9
- Trimmomatic9
- Bandage8
- FASTX-Toolkit8
- BCFtools7
- BamTools7
- Biopython7
- HISAT27
- RDMkit7
- Trim Galore7
- msConvert7
- seqtk7
- Flye6
- MAFFT6
- MaxQuant6
- Minimap26
- Ontology Lookup Service6
- Open Babel6
- Unicycler6
- Workflow4Metabolomics6
- gffread6
- BridgeDb5
- COPASI5
- DESeq25
- 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
- European Nucleotide Archive (ENA)4
- GOseq4
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- MACS4
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- Merqury4
- Newick Utilities4
- QualiMap4
- The Protein Data Bank (PDB)4
- UniProt4
- bx-python4
- mothur4
- snpEff4
- Apollo3
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- Bracken3
- BridgeDbR3
- Cardinal3
- Clustal 1.8 (Clustal W, Clustal X)3
- DISEASES3
- DropletUtils3
- FastTree3
- GenomeScope 2.03
- GraPhlAn3
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- NCBI Gene4
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- OBO Foundry2
- Ontology Lookup Service2
- PRoteomics IDEntifications database2
- RDA DMP Common Standard for Machine-Actionable Data Management Plans2
- 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
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- Datanator1
- FAIR sharing1
- FAIRtracks1
- Gene3D1
- Genomics England | PanelApp1
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- IUPAC International Chemical Identifier1
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- 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
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- Worldwide Protein Data Bank1
- Zenodo 1
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- Khan Academy Statistics32
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- Coding for Reproducible Research (CfRR)19
- Coursera19
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- CINECA PROJECT17
- CSC - IT Center for Science12
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- Genome 3D8
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- BioData.pt6
- Data Steward team Ghent University6
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- LIPID MAPS5
- UNIVERSE-HPC project5
- COG-Train4
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- University of Cambridge Bioinformatics Training4
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- Hochschule140
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- RNA-seq128
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- jupyter-notebook85
- Machine learning82
- Reproducibility82
- digital gestützte Lehre82
- OER80
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- Educación física77
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- Creative Commons Attribution Non Commercial Share Alike 4.0 International713
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- MIT License161
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- GNU General Public License v3.0 only53
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- Apache License 2.021
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- Other (Non-Commercial)15
- Other (Attribution)6
- Creative Commons Attribution 1.0 Generic5
- CeCILL Free Software License Agreement v2.13
- Other (Open)3
- Artistic License 2.02
- GNU Affero General Public License v3.0 only2
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- Target audience
- Students585
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- PhD students228
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- Graduate Students82
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- PhD candidate26
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- PhD candidates23
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- scientists22
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- beamtime users, researchers, PhD students21
- Bench biologists20
- life scientists20
- Data Managers18
- Academia/ Research Institution17
- Industry17
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- PhD Students17
- researchers17
- Beginners16
- Data Scientist16
- Data Scientists16
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- ExPaNDS and PaNOSC project members15
- Healthcare15
- data stewards15
- health professionals13
- Researcher in life sciences13
- Computational biologists12
- Master students12
- Research Scientists12
- biologists12
- data managers12
- healthcare professionals12
- software developers, bioinformaticians12
- Biomedical Researchers11
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- Clinical Scientists6
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- computational scientists6
- engineers6
- plant researchers6
- postdocs6
- General Interest5
- archaeologists5
- crystallography5
- genomics researchers5
- material scientists5
- neutron community5
- postgrad5
- Anyone wishing to use bioinformatics resources to find basic information about a virus.4
- Biologists with little or no prior computational experience4
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- PI4
- 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
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- Helena Rasche128
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- Plazi Verein29
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- Nate Coraor27
- Subina Mehta27
- John Chilton25
- Nicola Soranzo25
- Teaching materials at the Harvard Chan Bioinformatics Core25
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- Egon Willighagen22
- NBIS - National Bioinformatics Infrastructure Sweden22
- Anne Fouilloux21
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- Michelle Brazas21
- posit-conf-202321
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- Bazante Sanders18
- Katarzyna Kamieniecka18
- Krzysztof Poterlowicz18
- Laura Cooper18
- Terri Attwood18
- UC Davis Bioinformatics Core Training Page18
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- Mehmet Tekman17
- Sergio Martínez Cuesta17
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- Donny Vrins13
- Fred Hutch Data Science Lab13
- James Johnson13
- Katherine Do13
- Monique Zahn13
- Wolfgang Maier13
- Andrew Mason12
- Anup Kumar12
- Celia van Gelder12
- Jenny Drnevich @jenny12
- Marius van den Beek12
- Melanie Föll12
- Patricia Palagi12
- Personalized Health Informatics Group12
- Simon Andrews12
- Simon Bray12
- Allegra Via11
- Geert van Geest11
- Khaled Jum'ah11
- Mathieu Bourgey11
- Pavankumar Videm11
- Sundeep Agarwal11
- Various11
- Canadian Bioinformatics Workshops10
- Daniel Blankenberg10
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- Martin Čech10
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- Avans Hogeschool9
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- Anthony Bretaudeau108
- Cristóbal Gallardo104
- Niall Beard90
- Toby Hodges83
- Wendi Bacon77
- Nate Coraor70
- François Michonneau69
- Armin Dadras66
- Pavankumar Videm65
- Erin Becker63
- Gildas Le Corguillé63
- Marius van den Beek62
- William Durand59
- Zhian N. Kamvar59
- Mine Cetinkaya-Rundel56
- Robert Andrews55
- Katrin Leinweber54
- Raniere Silva54
- Simon Gladman54
- Tracy Teal53
- W. Trevor King52
- Andy Boughton51
- maneesha51
- Beatriz Serrano-Solano49
- Katie Anne Mills48
- Maxim Belkin48
- Teresa Müller48
- Lucille Delisle46
- Mehmet Tekman46
- Yvan Le Bras46
- David Pérez-Suárez44
- Gabriel A. Devenyi44
- Canadian Bioinformatics Workshops43
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- Abby Cabunoc Mayes42
- EvanWill42
- Ian Lee42
- Jon Pipitone42
- Jonah Duckles42
- Michael Hansen42
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- Brandon Curtis41
- David Mawdsley41
- Greg Wilson41
- Jemma Stachelek41
- Remi Rampin41
- Allen Lee40
- Andrew Sanchez40
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- Jeff Oliver39
- Joel Nothman39
- Nick Young39
- naught10139
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- Rémi Emonet38
- William L. Close38
- Marie Josse37
- Rayna M Harris37
- Wolfgang Maier36
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- Sarah Brown35
- Anup Kumar34
- Gerard Capes34
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- K.E. Koziar29
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- Simon Bray28
- Subina Mehta28
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- Paula Andrea Martinez26
- Michael Joseph25
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- Geert van Geest24
- João Rodrigues24
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- Robert Davey22
- Sarah Stevens22
- Julia Jakiela21
- Tristan Reynolds21
- Wolmar Nyberg Åkerström21
- actions-user21
- Henry Schreiner20
- Hilmar Lapp20
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- Related resource
- Associated Training Datasets333
- Associated Workflows309
- Jupyter Notebook (with Solutions)54
- Jupyter Notebook (without Solutions)54
- Input datasets34
- Research Data Management in Life Sciences11
- Slides10
- Associated slides9
- The Carpentries7
- 2nd PaN EOSC Symposium6
- Development in Galaxy slides6
- Quarto/RMarkdown Notebook6
- Proteomics dataset5
- Sequence analysis dataset5
- Transcriptomics dataset5
- Assembly dataset4
- Variant Analysis dataset4
- Assembly slides3
- Associated deliverable on the ExPaNDS ontologies3
- DMPonline3
- Data Stewardship Wizard3
- MAX IV youtube channel3
- Part 33
- Part 43
- Workshop recording3
- ChIP-Seq data analysis dataset2
- DisProt2
- Epigenetics dataset2
- Galaxy Server administration slides2
- Genome Annotation dataset2
- McStas2
- Metagenomics dataset2
- OpenCloning2
- Part 22
- Part 52
- Part 62
- Part 72
- Part 82
- Part 92
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