Materials - PaN Training

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- Operation
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- Data visualisation15
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- Quality control5
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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
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- Classification1
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- Tool
- Galaxy372
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- FastQC36
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- fastp16
- scikit-learn16
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- 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
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- Minimap26
- Ontology Lookup Service6
- Open Babel6
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- Workflow4Metabolomics6
- gffread6
- BridgeDb5
- COPASI5
- DESeq25
- Galactic Circos5
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- 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
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- European Nucleotide Archive (ENA)4
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- bx-python4
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- Apollo3
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- BridgeDbR3
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- 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
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- 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
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- BridgeDb1
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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
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- CSC - IT Center for Science12
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- Creative Commons Attribution Non Commercial Share Alike 4.0 International713
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- Apache License 2.021
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- CeCILL Free Software License Agreement v2.13
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- Target audience
- Students587
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- scientists22
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- beamtime users, researchers, PhD students21
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- Data Managers18
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- researchers17
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- Healthcare15
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- 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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- postdocs6
- General Interest5
- archaeologists5
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- material scientists5
- neutron community5
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- 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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- John Chilton25
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- Teaching materials at the Harvard Chan Bioinformatics Core25
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- posit-conf-202321
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- Laura Cooper18
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- Fred Hutch Data Science Lab13
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- Wolfgang Maier13
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- Anup Kumar12
- Celia van Gelder12
- Jenny Drnevich @jenny12
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- Melanie Föll12
- Patricia Palagi12
- Personalized Health Informatics Group12
- Simon Andrews12
- Simon Bray12
- Allegra Via11
- Geert van Geest11
- Khaled Jum'ah11
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- Pavankumar Videm11
- Sundeep Agarwal11
- Various11
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- Cristóbal Gallardo104
- Niall Beard90
- Toby Hodges83
- Wendi Bacon78
- Nate Coraor71
- 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
- Simon Gladman55
- Katrin Leinweber54
- Raniere Silva54
- Tracy Teal53
- W. Trevor King52
- Andy Boughton51
- maneesha51
- Beatriz Serrano-Solano49
- Katie Anne Mills48
- Maxim Belkin48
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- Mehmet Tekman46
- Yvan Le Bras46
- David Pérez-Suárez44
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- Canadian Bioinformatics Workshops43
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- Remi Rampin41
- Allen Lee40
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- Rayna M Harris37
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- Sarah Stevens22
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- Henry Schreiner20
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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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