Materials - Bioconductor

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- Personal genomics
- Data management264
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- FAIR data200
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- Metagenomics82
- Shotgun metagenomics82
- Bottom-up proteomics77
- Discovery proteomics77
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- Protein and peptide identification77
- Proteomics77
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- Targeted proteomics77
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- Biodiversity73
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- Single-cell genomics62
- Single-cell sequencing62
- Antimicrobial stewardship56
- Medical microbiology56
- Microbial genetics56
- Microbial physiology56
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- Operation
- Data handling1
- Database retrieval1
- File handling1
- File processing1
- Functional genome annotation1
- Genome annotation1
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- Processing1
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- Galaxy47
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- BUSCO8
- Bioconductor8
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- Minimap24
- gffread4
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- BEDTools3
- Bwa-mem23
- Cutadapt3
- Diamond3
- Flye3
- GenomeScope 2.03
- MultiQC3
- OMArk3
- STAR3
- gfastats3
- snippy3
- BCFtools2
- BLAST2
- Bakta2
- Bowtie2
- Bracken2
- COMBAT-TB Workbench2
- Clustal 1.8 (Clustal W, Clustal X)2
- DeepTools2
- Falco2
- GECKO2
- Helixer2
- InterProScan (EBI)2
- MAGeCK2
- Merqury2
- NanoPlot2
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- SAMtools2
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- eggNOG-mapper v22
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- tbl2gff32
- AUGUSTUS1
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- UCSC Genome Browser1
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- bx-python1
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- dRep1
- funannotate1
- ggplot21
- kraken21
- orfipy1
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- Keyword
- Genomics125
- Next generation sequencing46
- Genome Annotation31
- Variant analysis26
- Genome assembly20
- RNA-seq20
- microgalaxy20
- R17
- Transcriptomics17
- biodiversity16
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- jbrowse113
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- Unix/Linux12
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- General9
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- ATAC-seq5
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- Galaxy5
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- assembly5
- bacteria5
- illumina5
- work-in-progress5
- ChIP-seq4
- Cloud computing4
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- Quality Control4
- Version control4
- eLearning4
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- Assembly Evaluation3
- Database Management3
- Evolution3
- FAIR data3
- Machine learning3
- Multiomics3
- Python3
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- Variant Analysis3
- apollo23
- bioinformatics3
- essential genes3
- eukaryota3
- plants3
- Annotation2
- Artificial intelligence2
- Braker32
- Command line2
- Data analysis2
- FEGA2
- Federated EGA2
- Functional Genomics2
- HPC2
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- Pathways and Networks2
- Phylogenetics / Phylogenomics2
- Shell2
- amr2
- evolution2
- genomics2
- maker2
- nanopore2
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- tnseq2
- transcriptomics2
- RNA-Seq1
- API1
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- Not specified153
- Beginner47
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- License Not Specified106
- Creative Commons Attribution 4.0 International75
- GNU General Public License v3.0 only11
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- Creative Commons Attribution Non Commercial No Derivatives 4.0 International5
- Creative Commons Zero v1.0 Universal4
- Creative Commons Attribution Non Commercial 4.0 International1
- Creative Commons Attribution Share Alike 4.0 International1
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- Target audience
- Students52
- Clinicians6
- PhD students6
- Researchers6
- Biologists4
- Bioinformatician3
- Clinical Scientists3
- Bioinformaticians2
- Graduate students2
- Life Science Researchers2
- PhD Students2
- life scientists2
- Bioinformatician, Bioanalysts1
- Biologists with little or no prior computational experience1
- Biologists, Genomicists, Computer Scientists1
- Data Access Committeses from the EGA1
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- Master students1
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- PhD candidates1
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- Post Docs1
- Post docs1
- Postgraduate students1
- Principal Investigators1
- Principal Investigators (PIs)1
- Professors1
- Public Health Professionals1
- Researchers and bioinformaticians in other projects interested in depositiong data at the EGA1
- Researchers and bioinformaticians involved in the VEIS project1
- Scientists1
- Students, postdocs, and researchers, from any scientific environment (academia, facilities, companies, etc.) interested in viral data, as well as anyone looking for virion and viral genome images for use in teaching or publications.1
- beginner bioinformaticians1
- clinicians and informaticians interested in cancer genetics1
- data curators1
- genomics researchers1
- plant researchers1
- tool developers1
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- Author
- Anthony Bretaudeau13
- Bérénice Batut12
- Delphine Lariviere8
- Data Carpentry6
- bioinformatics.ca6
- Anna Syme5
- Anton Nekrutenko5
- Simon Gladman5
- Helena Rasche4
- Hélène Chiapello4
- Martin Morgan4
- The Gulbenkian Training Programme in Bioinformatics4
- Valentin Loux4
- Bazante Sanders3
- Canadian Bioinformatics Workshops3
- NBIS - National Bioinformatics Infrastructure Sweden3
- Romane LIBOUBAN3
- SIB Swiss Institute of Bioinformatics3
- Stéphanie Robin3
- Torsten Seemann3
- Alex Ostrovsky2
- Alexandre Cormier2
- Annabel Cansdale2
- Bioinformatics, Rockefeller University2
- Boas Pucker2
- Christoph Stritt2
- Cristóbal Gallardo2
- Daniela Brites2
- Emma Rand2
- Erwan Corre2
- Esteban Perez-Wohlfeil2
- Evelyn Greeves2
- Galo A. Goig2
- Hervé Pagès2
- Jorge Buenabad-Chavez2
- Laura Leroi2
- Maria Doyle2
- Mateo Boudet2
- Michael Lawrence2
- Nathan Dunn2
- Sarah Forrester2
- The Carpentries Lab2
- Alli Black1
- Andries Marees1
- Anika Erxleben1
- Applied Genomics1
- Biocore@CRG1
- Biodiversity Genomics Academy 20231
- BiotrAIn1
- Björn Grüning1
- Brandon Pickett1
- CRUK CI Bioinformatics Core1
- Christophe Antoniewski1
- Clea Siguret1
- Computational Genomics with R1
- Computational Metagenomics1
- Didier Debroas1
- Dipannita Ghosh1
- Egon Willighagen1
- Eija Korpelainen1
- Ellen McDonagh1
- Eric C. Anderson1
- Erik Hjerde1
- Espen Aberg1
- Espen Mikal Robertsen1
- Espen Åberg1
- Fabian Recktenwald1
- Federico Bianchini1
- Fred Hutch Data Science Lab1
- Friederike Ehrhart1
- Functional Genomics Laboratory1
- Giulio Formenti1
- Global Biodiversity Information Facility1
- Guillaume Gautreau1
- IB-ULFRI1
- Illimar Rekand1
- Jan Paces1
- Johann Confais1
- Jonathan Kreplak1
- Jonathan Mélius1
- Jordi Rambla1
- Juha Tornroos1
- Katharina Hoff1
- Kenji Fujihara1
- Keywan Hassani-Pak1
- Klaas Vandepoele1
- Korbinian Bösl1
- Kristyna Kupkova1
- Leonardo Collado-Torres1
- Linelle Abueg1
- Luca Cozzuto1
- Mahul Chakraborty1
- Marc Christian Heuermann1
- Marcella Sozzoni1
- Maria Lehtivaara1
- Marko Petek1
- Melbourne Bioinformatics1
- Michael Squance1
- Michiel Van Bel1
- Mike Lee1
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- Contributor
- Saskia Hiltemann41
- Bérénice Batut38
- Helena Rasche36
- Björn Grüning35
- Anthony Bretaudeau28
- Cristóbal Gallardo12
- Canadian Bioinformatics Workshops8
- Deepti Varshney8
- Erin Becker8
- François Michonneau8
- Nicola Soranzo8
- Toby Hodges8
- maneesha8
- Jason Williams7
- Niall Beard7
- Tracy Teal7
- Tristan Reynolds7
- Zhian N. Kamvar7
- Bianca Peterson6
- C. Titus Brown6
- Delphine Lariviere6
- Taylor Reiter6
- Teresa Müller6
- Amanda Charbonneau5
- Anna Syme5
- Anton Nekrutenko5
- Dan Kerchner5
- Mark Fernandes5
- Rayna M Harris5
- Robert Davey5
- Stéphanie Robin5
- Wolfgang Maier5
- Anita Schürch4
- Gildas Le Corguillé4
- Nelly Sélem4
- Pete4
- Peter van Heusden4
- Sarah Stevens4
- Simon Bray4
- The Gulbenkian Training Programme in Bioinformatics4
- Annajiat Alim Rasel3
- Bazante Sanders3
- Bob Freeman3
- Brittany N. Lasseigne, PhD3
- David Pérez-Suárez3
- Fotis E. Psomopoulos3
- Hilmar Lapp3
- JCSzamosi3
- Jemma Stachelek3
- Kari L. Jordan, PhD3
- Katrin Leinweber3
- Maria Doyle3
- Miaomiao Zhou3
- Michael R. Crusoe3
- Naupaka Zimmerman3
- Niclas Jareborg3
- Paul Zierep3
- Paula Andrea Martinez3
- Romane LIBOUBAN3
- Sam Nooij3
- Sarah Brown3
- Simon Gladman3
- Solenne Correard3
- William Durand3
- murraycadzow3
- zhibinlu3
- Aaron E. Jaime2
- Abby Cabunoc Mayes2
- AbrahamAvelar2
- Ahmed Moustafa2
- Alana Alexander2
- Allen Lee2
- Andrew Sanchez2
- Andy Boughton2
- Aziz Khan2
- Boas Pucker2
- Brandon Curtis2
- Charlie Barclay2
- Chris Miller2
- Christina K.2
- Christoph Stritt2
- CladoniaRang2
- Clara2
- Claudia Zirión Martínez2
- Clea Siguret2
- Darian2
- David Mawdsley2
- Dinindu Senanayake2
- EWheeler1232
- Edmund Miller2
- Emma Barnes2
- Erik Garrison2
- Esteban Perez-Wohlfeil2
- EvanWill2
- Finlay Maguire2
- Flavio Lombardo2
- Gabriel A. Devenyi2
- Geert van Geest2
- Graeme Grimes2
- Hadrien Gourlé2
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- e-learning50
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- slides6
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- Installation instructions1
- Manual1
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- Related resource
- Associated Training Datasets46
- Associated Workflows41
- Beacon v2: a discovery tool for genomic and pheno-clinical data1
- DisGeNET: a discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases1
- GPAP: the RD-Connect Genome-Phenome Analysis Platform for diagnosis and gene discovery in rare disease research1
- Genomics England PanelApp1
- Introduction to the EGA and sharing sensitive data1
- REPET image Docker1
- 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
- VEIS webinar: The essentials of DUO codes | Presentation1
- VEIS webinar: The essentials of DUO codes | Video1
- Video of the course1
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- Collection
- VEIS - Value of the EGA for Industry and Society3
- ELIXIR Biodiversity Community2
- ELIXIR Federated Human Data Community2
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- Active10
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