Materials - Bioconductor

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- Scientific topic
- Genomes
- Data management254
- Metadata management254
- Research data management (RDM)254
- Genome annotation224
- Exomes203
- Genomics203
- Personal genomics203
- Synthetic genomics203
- Viral genomics203
- Whole genomes203
- FAIR data196
- Findable, accessible, interoperable, reusable data196
- Comparative transcriptomics187
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- R153
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- Python136
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- Statistics and probability135
- MicroRNA sequencing126
- RNA sequencing126
- RNA-Seq126
- RNA-Seq analysis126
- Small RNA sequencing126
- Small RNA-Seq126
- Small-Seq126
- Transcriptome profiling126
- WTSS126
- Whole transcriptome shotgun sequencing126
- miRNA-seq126
- Algorithms124
- Computer programming124
- Data structures124
- Programming languages124
- Software development124
- Software engineering124
- Chromosome walking106
- Clone verification106
- DNA-Seq106
- DNase-Seq106
- High throughput sequencing106
- High-throughput sequencing106
- NGS106
- NGS data analysis106
- Next gen sequencing106
- Next generation sequencing106
- Panels106
- Primer walking106
- Sanger sequencing106
- Sequencing106
- Targeted next-generation sequencing panels106
- Bioinformatics102
- Active learning100
- Ensembl learning100
- Kernel methods100
- Knowledge representation100
- Machine learning100
- Neural networks100
- Recommender system100
- Reinforcement learning100
- Supervised learning100
- Unsupervised learning100
- Metagenomics82
- Shotgun metagenomics82
- Biodiversity73
- Data rendering67
- Data visualisation67
- Bottom-up proteomics63
- Discovery proteomics63
- MS-based targeted proteomics63
- MS-based untargeted proteomics63
- Metaproteomics63
- Peptide identification63
- Protein and peptide identification63
- Proteomics63
- Quantitative proteomics63
- Targeted proteomics63
- Top-down proteomics63
- Single-cell genomics60
- Single-cell sequencing60
- Antimicrobial stewardship56
- Medical microbiology56
- Microbial genetics56
- Microbial physiology56
- Microbial surveillance56
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- Operation
- Data handling1
- Database retrieval1
- File handling1
- File processing1
- Functional genome annotation1
- Genome annotation1
- Metagenome annotation1
- Processing1
- Query1
- Query and retrieval1
- Report handling1
- Sequence classification1
- Structural genome annotation1
- Utility operation1
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- Tool
- Galaxy47
- JBrowse13
- BUSCO8
- FastQC6
- QUAST5
- Bandage4
- Minimap24
- gffread4
- Apollo3
- 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
- Recentrifuge2
- SAMtools2
- TRANSIT2
- eggNOG-mapper v22
- fastp2
- tbl2gff32
- AUGUSTUS1
- BWA1
- BamTools1
- BridgeDb1
- CheckM1
- Circos1
- Data Stewardship Wizard1
- FEELnc1
- FastTree1
- Filtlong1
- FreeBayes1
- GAEVAL1
- Galactic Circos1
- ISEScan1
- Integron Finder1
- Jvarkit1
- MAFFT1
- MAKER1
- Medaka1
- NCBI Datasets1
- NCBI Resources1
- PASTEClassifier1
- PPanGGOLiN1
- PlasmidFinder1
- Polypolish1
- QualiMap1
- RAxML1
- RDMkit1
- RED1
- REPET1
- REXdb1
- Racon1
- RapidNJ1
- RepeatMasker1
- RepeatModeler1
- Roary1
- SALSA1
- SNAP1
- SRA1
- Smudgeplots1
- Trimmomatic1
- UCSC Genome Browser1
- Unicycler1
- Vcflib1
- ViralZone1
- antiSMASH1
- bx-python1
- chemfp1
- compute_sequence_length1
- dRep1
- funannotate1
- ggplot21
- kraken21
- orfipy1
- purge_dups1
- shovill1
- staramr1
- tb-profiler1
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- Standard database or policy
- European Nucleotide Archive1
- FAIRsharing1
- Genomics England | PanelApp1
- RDA DMP Common Standard for Machine-Actionable Data Management Plans1
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- Content provider
- Glittr.org77
- GTN50
- ERGA Knowledge Hub41
- European Bioinformatics Institute (EBI)13
- Centre for Genomic Regulation (CRG)3
- ELIXIR Norway3
- ELIXIR2
- ELIXIR Slovenia2
- Cloud-SPAN1
- Department of Bioinformatics - BiGCaT, Maastricht University1
- ELIXIR-SI eLearning Platform (EeLP)1
- EOSC4Cancer1
- IFB French Institute of Bioinformatics1
- SIB Swiss Institute of Bioinformatics1
- VHP4Safety1
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- Keyword
- Genomics125
- Next generation sequencing46
- Genome Annotation31
- Variant analysis26
- Genome assembly20
- RNA-seq20
- microgalaxy20
- R17
- Transcriptomics17
- biodiversity16
- prokaryote15
- Long read sequencing14
- jbrowse113
- Genome annotation12
- Unix/Linux12
- Assembly11
- gmod11
- Comparative genomics10
- General9
- eukaryote9
- Data visualization8
- Epigenetics7
- Metagenomics7
- High performance computing6
- Population genetics6
- Single-cell sequencing6
- ATAC-seq5
- Data management5
- Galaxy5
- Statistics5
- assembly5
- bacteria5
- illumina5
- work-in-progress5
- ChIP-seq4
- Cloud computing4
- EeLP4
- Epidemiology4
- Quality Control4
- Version control4
- eLearning4
- one-health4
- Assembly Evaluation3
- Database Management3
- Evolution3
- FAIR data3
- Machine learning3
- Multiomics3
- Python3
- Reproducibility3
- Variant Analysis3
- apollo23
- bioinformatics3
- essential genes3
- eukaryota3
- plants3
- Annotation2
- Artificial intelligence2
- Braker32
- Command line2
- Data analysis2
- FEGA2
- Federated EGA2
- Functional Genomics2
- HPC2
- Microbiology2
- Pathways and Networks2
- Phylogenetics / Phylogenomics2
- Shell2
- amr2
- evolution2
- genomics2
- maker2
- nanopore2
- pacbio2
- tnseq2
- transcriptomics2
- RNA-Seq1
- API1
- Amazon Web Services1
- Assembly Curation1
- Biocuration1
- Bioinformatics1
- BridgeDb1
- CRISPR1
- CWL1
- ChIP-Seq1
- Conservation genomics1
- Containerization1
- Data Analysis1
- Data Life Cycle1
- Data Management Plan1
- Data Steward1
- Data Stewardship Wizard1
- Data management planning1
- Data science1
- Data sharing1
- Data submission1
- Designing functional genomics experiments1
- Docker1
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- Competency level
- Not specified142
- Beginner47
- Intermediate13
- Advanced1
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- Licence
- License Not Specified95
- Creative Commons Attribution 4.0 International75
- GNU General Public License v3.0 only11
- MIT License11
- 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
- Researchers6
- Clinicians5
- PhD students5
- Biologists4
- Bioinformatician3
- Bioinformaticians2
- Clinical Scientists2
- 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
- Data Managers1
- Data Scientists1
- Data stewards1
- Life Scientists1
- Master students1
- Microbiologists1
- 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 members1
- PhD candidates1
- PhD students in Genomics datascience1
- 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
- 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
- Jorge Buenabad-Chavez2
- Laura Leroi2
- Maria Doyle2
- Mateo Boudet2
- 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
- Michiel Van Bel1
- Mike Lee1
- Monique Zahn1
- Nadia Goué1
- Nanopore for Educators1
- Nazeefa Fatima1
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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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- Resource type
- e-learning49
- Recorded webinar10
- Video8
- Training materials7
- Slides6
- slides6
- Tutorial5
- course materials5
- Presentation4
- Webinar2
- Bioinformatics1
- Course materials1
- Installation instructions1
- Manual1
- Online material1
- Scripts1
- knowledgebase1
- online course1
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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
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- Collection
- ELIXIR Biodiversity Community2
- ELIXIR Federated Human Data Community2
- VEIS - Value of the EGA for Industry and Society2
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- Status
- Active10
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