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Merge pull request #36 from mblue9/add-carpentries-code
Add carpentries code
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| name: Render and Publish | ||
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| on: | ||
| push: | ||
| branches: [devel] | ||
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| jobs: | ||
| build-deploy: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| contents: write | ||
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| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
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| - name: Set up Quarto | ||
| uses: quarto-dev/quarto-actions/setup@v2 | ||
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| # Install necessary system dependencies | ||
| - name: Install system dependencies | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev | ||
| # Add R dependencies | ||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
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| - name: Install R dependencies | ||
| run: Rscript -e 'install.packages(c("evaluate", "rmarkdown", "readr", "tidyr", "reactable", "maps", "plotly", "ggplot2", "tidygeocoder"))' | ||
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| - name: Publish to GitHub Pages (and render) | ||
| uses: quarto-dev/quarto-actions/publish@v2 | ||
| with: | ||
| target: gh-pages | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # GitHub token secret for publishing |
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|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| project: | ||
| type: website | ||
| output-dir: docs | ||
| render: | ||
| - "*.qmd" | ||
| website: | ||
| title: "Bioconductor Teaching" | ||
| navbar: | ||
| background: "#3792ad" # Bioconductor.org blue | ||
| left: | ||
| - text: "Instructors" | ||
| href: carpentries/instructors.qmd | ||
| - text: "Workshops" | ||
| href: carpentries/workshops.qmd | ||
| format: | ||
| html: | ||
| embed-resources: false |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,53 +1,57 @@ | ||
| name institution city status country | ||
| Laurent Gatto UCLouvain Brussels Certified Belgium | ||
| Charlotte Soneson Friedrich Miescher Institute for Biomedical Research Basel Certified Switzerland | ||
| Kevin Rue-Albrecht University of Oxford Oxford Certified United Kingdom | ||
| Robert Castelo Pompeu Fabra University Barcelona Certified Spain | ||
| Kozo Nishida Tokyo University of Agriculture and Technology Tokyo Certified Japan | ||
| Peter Hickey WEHI Melbourne Certified Australia | ||
| Saskia Freytag WEHI Melbourne Certified Australia | ||
| Helen Lindsay CHUV Lausanne Certified Switzerland | ||
| Jenny Drnevich University of Illinois Urbana Certified United States | ||
| Pariksheet Nanda University of Michigan Medical School Ann Arbor Certified United States | ||
| Marcel Ramos CUNY New York Certified United States | ||
| Liz Ing-Simmons MRC London Institute of Medical Sciences London Certified United Kingdom | ||
| Nitesh Turaga Bioconductor Community Buffalo Certified United States | ||
| Lisa Breckels University of Cambridge Cambridge Certified United States | ||
| Kayla Interdonato Roswell Park Comprehensive Cancer Center Buffalo Certified United States | ||
| Mikhail Dozmorov Virginia Commonwealth University Richmond Certified United States | ||
| Susan Holmes Stanford University Stanford Certified United States | ||
| Sonia Barasa Pan-African Mosquito Control Association (PAMCA) Nairobi Certified Kenya | ||
| Maureen Osano Kenya Medical Research Institute (KEMRI) Nairobi Certified Kenya | ||
| Javier Carpinteyro-Ponce Carnegie Institution for Science Maryland Certified United States | ||
| Fabricio Almeida-Silva VIB-UGent Center for Plant Systems Biology Ghent Certified - CZI Year 1 Belgium | ||
| Anand Ruban Agarvas University Hospital Heidelberg Heidelberg Certified - CZI Year 1 Germany | ||
| Oliver Crook University of Oxford Oxford Certified - CZI Year 1 United Kingdom | ||
| Almut Lütge University of Zürich Zurich Certified - CZI Year 1 Switzerland | ||
| Leo Lahti University of Turku Turku Certified - CZI Year 1 Finland | ||
| Sehyun Oh City University of New York New York Certified - CZI Year 1 United States | ||
| Umar Ahmad Bauchi State University Gadau In Progress Nigeria | ||
| Chia Sin Liew University of Nebraska-Lincoln Nebraska Certified - CZI Year 1 United States | ||
| Charlotte Hutchings University of Cambridge Cambridge Certified - CZI Year 1 United States | ||
| Roberto Carlos Álvarez Martínez Universidad Autonoma de Queretaro Mexico In Progress Mexico | ||
| David Shih University of Hong Kong Hong Kong Certified - CZI Year 1 China | ||
| Rodrigo Arcoverde Cerveira da Silva Karolinska Institute Stockholm Certified - CZI Year 1 Sweden | ||
| Javier Carpinteyro Ponce University of Maryland Maryland Certified - CZI Year 1 United States | ||
| Zuguang Gu German Cancer Research Center Heidelberg Certified - CZI Year 1 Germany | ||
| Givanna Putri Walter and Eliza Hall Institute of Medical Research Melbourne Certified - CZI Year 1 Australia | ||
| Zedias Chikwambi Chinhoyi University of Technology Chinhoyi Certified - CZI Year 1 Zimbabwe | ||
| Pageneck Chikondowa African Institute of Biomedical Science and Technology Harare Certified - CZI Year 1 Zimbabwe | ||
| Marie Hidjo African Institute of Biomedical Science and Technology Harare Certified - CZI Year 1 Zimbabwe | ||
| Kevin Stachelek University of Southern California Los Angeles In Progress United States | ||
| Erick Isaac Navarro Delgado University of British Columbia Vancouver In Progress Canada | ||
| Pedro Baldoni Walter and Eliza Hall Institute of Medical Research Melbourne Certified - CZI Year 2 Australia | ||
| Princess Rodriguez University of Vermont Burlington In Progress United States | ||
| Tim Triche Van Andel Institute Grand Rapids Certified - CZI Year 2 United States | ||
| Izabela Mamede Universidade Federal de Minas Gerais Belo Horizonte Certified - CZI Year 2 Brazil | ||
| Jacques Serizay Institut Pasteur Paris In Progress France | ||
| Robert Ivanek University of Basel, Swiss Institute of Bioinformatics Basel Certified - CZI Year 2 Switzerland | ||
| Hamdi Furkan Kepenek Abdullah Gül University Kayseri In Progress Turkey | ||
| 陈秭如 GuangZhou Lab Guangzhou In Progress China | ||
| Amal Boukteb National Institute for Agricultural Research of Tunisia (INRAT) Tunis Certified - CZI Year 2 Tunisia | ||
| Arnab Mukherjee Manipal Institute of Technology Manipal Certified - CZI Year 2 India | ||
| Harvinder Singh Department of Translational and Regenerative Medicine, PGIMER Chandigarh In Progress India | ||
| Janani Ravi University of Colorado Anschutz Medical Campus Aurora In Progress United States | ||
| name www institution city country status | ||
| Laurent Gatto https://lgatto.github.io/about/ UCLouvain Brussels Belgium Certified | ||
| Charlotte Soneson https://csoneson.github.io/ Friedrich Miescher Institute for Biomedical Research Basel Switzerland Certified | ||
| Kevin Rue-Albrecht https://kevinrue.github.io/ University of Oxford Oxford United Kingdom Certified | ||
| Robert Castelo https://functionalgenomics.upf.edu Pompeu Fabra University Barcelona Spain Certified | ||
| Kozo Nishida https://github.com/kozo2 Tokyo University of Agriculture and Technology Tokyo Japan Certified | ||
| Peter Hickey https://www.peterhickey.org/ WEHI Melbourne Australia Certified | ||
| Saskia Freytag https://www.wehi.edu.au/people/saskia-freytag WEHI Melbourne Australia Certified | ||
| Helen Lindsay https://www.chuv.ch/en/bdsc/about-us CHUV Lausanne Switzerland Certified | ||
| Jenny Drnevich https://hpcbio.illinois.edu/people University of Illinois Urbana United States Certified | ||
| Pariksheet Nanda https://medicine.umich.edu/dept/microbiology-immunology/pariksheet-nanda-phd-0 University of Michigan Medical School Ann Arbor United States Certified | ||
| Marcel Ramos https://cunyisph.org/team/marcel-ramos/ CUNY New York United States Certified | ||
| Liz Ing-Simmons https://liz.rbind.io/ MRC London Institute of Medical Sciences London United Kingdom Certified | ||
| Nitesh Turaga https://niteshturaga.com/ Bioconductor Community Buffalo United States Certified | ||
| Lisa Breckels https://lmsimp.github.io/ University of Cambridge Cambridge United States Certified | ||
| Kayla Interdonato Roswell Park Comprehensive Cancer Center Buffalo United States Certified | ||
| Mikhail Dozmorov https://dozmorovlab.github.io/ Virginia Commonwealth University Richmond United States Certified | ||
| Susan Holmes https://susan.su.domains/ Stanford University Stanford United States Certified | ||
| Sonia Barasa Pan-African Mosquito Control Association (PAMCA) Nairobi Kenya Certified | ||
| Maureen Osano Kenya Medical Research Institute (KEMRI) Nairobi Kenya Certified | ||
| Javier Carpinteyro-Ponce https://bse.carnegiescience.edu/javier-carpinteyro-ponce Carnegie Institution for Science Maryland United States Certified | ||
| Fabricio Almeida-Silva VIB-UGent Center for Plant Systems Biology Ghent Belgium Certified - CZI Year 1 | ||
| Anand Ruban Agarvas University Hospital Heidelberg Heidelberg Germany Certified - CZI Year 1 | ||
| Oliver Crook University of Oxford Oxford United Kingdom Certified - CZI Year 1 | ||
| Almut Lütge University of Zürich Zurich Switzerland Certified - CZI Year 1 | ||
| Leo Lahti University of Turku Turku Finland Certified - CZI Year 1 | ||
| Sehyun Oh City University of New York New York United States Certified - CZI Year 1 | ||
| Umar Ahmad Bauchi State University Gadau Nigeria In Progress | ||
| Chia Sin Liew University of Nebraska-Lincoln Nebraska United States Certified - CZI Year 1 | ||
| Charlotte Hutchings University of Cambridge Cambridge United States Certified - CZI Year 1 | ||
| Roberto Carlos Álvarez Martínez Universidad Autonoma de Queretaro Mexico Mexico In Progress | ||
| David Shih University of Hong Kong Hong Kong China Certified - CZI Year 1 | ||
| Rodrigo Arcoverde Cerveira da Silva Karolinska Institute Stockholm Sweden Certified - CZI Year 1 | ||
| Javier Carpinteyro Ponce University of Maryland Maryland United States Certified - CZI Year 1 | ||
| Zuguang Gu German Cancer Research Center Heidelberg Germany Certified - CZI Year 1 | ||
| Givanna Putri Walter and Eliza Hall Institute of Medical Research Melbourne Australia Certified - CZI Year 1 | ||
| Zedias Chikwambi Chinhoyi University of Technology Chinhoyi Zimbabwe Certified - CZI Year 1 | ||
| Pageneck Chikondowa African Institute of Biomedical Science and Technology Harare Zimbabwe Certified - CZI Year 1 | ||
| Marie Hidjo African Institute of Biomedical Science and Technology Harare Zimbabwe Certified - CZI Year 1 | ||
| Kevin Stachelek University of Southern California Los Angeles United States Certified - CZI Year 2 | ||
| Erick Isaac Navarro Delgado University of British Columbia Vancouver Canada Certified - CZI Year 2 | ||
| Pedro Baldoni University of Pittsburgh Pittsburgh United States Certified - CZI Year 2 | ||
| Princess Rodriguez University of Vermont Burlington United States In Progress | ||
| Tim Triche Van Andel Institute Grand Rapids United States Certified - CZI Year 2 | ||
| Izabela Mamede Universidade Federal de Minas Gerais Belo Horizonte Brazil Certified - CZI Year 2 | ||
| Jacques Serizay Institut Pasteur Paris France In Progress | ||
| Robert Ivanek "University of Basel, Swiss Institute of Bioinformatics" Basel Switzerland Certified - CZI Year 2 | ||
| Hamdi Furkan Kepenek Abdullah Gül University Kayseri Turkey In Progress | ||
| Ziru Chen GuangZhou Lab Guangzhou China In Progress | ||
| Amal Boukteb National Institute for Agricultural Research of Tunisia (INRAT) Tunis Tunisia Certified - CZI Year 2 | ||
| Arnab Mukherjee Manipal Institute of Technology Manipal India Certified - CZI Year 2 | ||
| Harvinder Singh "Department of Translational and Regenerative Medicine, PGIMER" Chandigarh India Certified - CZI Year 2 | ||
| Janani Ravi University of Colorado Anschutz Medical Campus Aurora United States In Progress | ||
| Guerrino Macori University College Dublin Dublin Ireland Certified | ||
| Ouso Daniel https://www.linkedin.com/in/ousodaniel/ University College Dublin Dublin Ireland Certified | ||
| Amit Mandal University of Oxford Oxford United Kingdom Certified | ||
| Michael Landi International Institute of Tropical Agriculture (IITA) Nairobi Kenya Certified |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,20 +1,24 @@ | ||
| date hosted_by workshop city instructors country | ||
| March 2024 University of Illinois bioc-intro Champaign Jenny Drnevich, Negin Valizadegan, Yifei Kang United States | ||
| November 2023 Instituto Evandro Chagas bioc-rnaseq Belém Rodrigo Arcoverde Cerveira da Silva Brazil | ||
| 15 October 2023 BioCAsia2023 bioc-rnaseq Hong Kong David Shih China | ||
| 12-13 October 2023 Carnegie Institution bioc-rnaseq Baltimore Javier Carpinteyro-Ponce, Frederick Tan United States | ||
| 9-12 October 2023 University of Bergen bioc-intro Bergen Leo Lahti Norway | ||
| October 2023 University of Illinois bioc-intro Champaign Jenny Drnevich, Jessica Holmes, Yifei Kang United States | ||
| 18-19 September 2023 EuroBioC2023 bioc-rnaseq Ghent Soneson Charlotte, Almut Lütge, Fabricio Almeida-Silva Belgium | ||
| 18-19 September 2023 EuroBioC2023 bioc-intro Ghent Laurent Gatto, Charlotte Hutchings, Olly Crook, Givanna Putri, Marcel Ramos Pérez Belgium | ||
| 31 July-1 August 2023 BioC2023 bioc-intro Boston Jenny Drnevich, Sehyun Oh United States | ||
| 19-21 June 2023 University of Oulu bioc-intro Oulu Leo Lahti Finland | ||
| March 2023 University of Illinois bioc-intro Champaign Jenny Drnevich, Jessica Holmes, Negin Valizadegan United States | ||
| March 2023 UCLouvain bioc-intro Brussels Laurent Gatto Belgium | ||
| 21-24 Feb 2023 Savitribai Phule Pune University bioc-intro Pune Leo Lahti India | ||
| 2023 NA bioc-intro Uzhhorod Laurent Gatto Ukraine | ||
| 12-13 September 2022 EuroBioC2022 bioc-intro Heidelberg Charlotte Soneson, Laurent Gatto Germany | ||
| 2022 UCLouvain bioc-intro Brussels Laurent Gatto Belgium | ||
| July 2024 BioC2024 bioc-rnaseq Grand Rapids Jenny Drnevich, Tim Triche, Charllote Hutchings United States | ||
| September 2024 EuroBioC2024 bioc-intro Oxford Oliver Crook, Marcel Ramos-Perez United Kingdom | ||
| September 2024 EuroBioC2024 bioc-rnaseq Oxford Fabricio Almeida-Silva, Robert Ivanek United Kingdom | ||
| date hosted_by host_url workshop workshop_url city country instructors | ||
| 2-3 September 2024 EuroBioC2024 https://eurobioc2024.bioconductor.org/ bioc-intro https://bioconductor.github.io/2024-09-02-BiocIntro-EuroBioc/ Oxford United Kingdom "Oliver Crook, Marcel Ramos-Perez" | ||
| 2-3 September 2024 EuroBioC2024 https://eurobioc2024.bioconductor.org/ bioc-rnaseq https://bioconductor.github.io/2024-09-02-RNASeq-EuroBioc/ Oxford United Kingdom "Fabricio Almeida-Silva, Robert Ivanek" | ||
| 22-23 July 2024 BioC2024 https://www.bioc2024.bioconductor.org/ bioc-rnaseq https://bioconductor.github.io/2024-07-22-BiocRnaseq-Bioc2024/ Grand Rapids United States "Jenny Drnevich, Tim Triche, Charlotte Hutchings" | ||
| 11-12 July 2024 Karolinska Institute https://ki.se/en bioc-rnaseq https://rodrigarc.github.io/2024-07-11-bioconductor-rnaseq/ Stockholm Sweden Rodrigo Arcoverde Cerveira da Silva | ||
| March 2024 University of Illinois https://illinois.edu/ bioc-intro Champaign United States "Jenny Drnevich, Negin Valizadegan, Yifei Kang" | ||
| November 2023 Instituto Evandro Chagas https://www.gov.br/iec/pt-br bioc-rnaseq Belém Brazil Rodrigo Arcoverde Cerveira da Silva | ||
| 15 October 2023 BioCAsia2023 https://biocasia2023.bioconductor.org bioc-rnaseq Hong Kong China David Shih | ||
| 12-13 October 2023 Carnegie Institution https://bse.carnegiescience.edu bioc-rnaseq Baltimore United States "Javier Carpinteyro-Ponce, Frederick Tan" | ||
| 9-12 October 2023 University of Bergen https://www.uib.no/en bioc-intro Bergen Norway Leo Lahti | ||
| October 2023 University of Illinois https://illinois.edu/ bioc-intro Champaign United States "Jenny Drnevich, Jessica Holmes, Yifei Kang" | ||
| 18-19 September 2023 EuroBioC2023 https://eurobioc2023.bioconductor.org/ bioc-rnaseq https://bioconductor.github.io/2023-09-18-RNASeq-EuroBioc/ Ghent Belgium "Soneson Charlotte, Almut Lütge, Fabricio Almeida-Silva" | ||
| 18-19 September 2023 EuroBioC2023 https://eurobioc2023.bioconductor.org/ bioc-intro https://bioconductor.github.io/2023-09-18-BiocIntro-EuroBioc/ Ghent Belgium "Laurent Gatto, Charlotte Hutchings, Olly Crook, Givanna Putri, Marcel Ramos Pérez" | ||
| 31 July-1 August 2023 BioC2023 https://bioc2023.bioconductor.org/ bioc-intro https://bioconductor.github.io/2023-07-31-BiocRnaseq-Bioc2023/ Boston United States "Jenny Drnevich, Sehyun Oh" | ||
| 19-21 June 2023 University of Oulu https://www.oulu.fi/en bioc-intro Oulu Finland Leo Lahti | ||
| 22-26 May 2023 Galaxy Smörgåsbord 2023 https://gallantries.github.io/video-library/events/smorgasbord3/ bioc-intro https://gallantries.github.io/video-library/modules/bioconductor Online Laurent Gatto | ||
| 22-26 May 2023 Galaxy Smörgåsbord 2023 https://gallantries.github.io/video-library/events/smorgasbord3/ bioc-project https://gallantries.github.io/video-library/modules/bioconductor Online Kevin Rue-Albrecht | ||
| March 2023 University of Illinois https://illinois.edu/ bioc-intro Champaign United States "Jenny Drnevich, Jessica Holmes, Negin Valizadegan" | ||
| March 2023 UCLouvain https://uclouvain.be/en/index.html bioc-intro Brussels Belgium Laurent Gatto | ||
| 21-24 Feb 2023 Savitribai Phule Pune University http://www.unipune.ac.in/ bioc-intro Pune India Leo Lahti | ||
| 2023 NA bioc-intro Uzhhorod Ukraine Laurent Gatto | ||
| 12-13 September 2022 EuroBioC2022 https://eurobioc2022.bioconductor.org/ bioc-intro https://bioconductor.github.io/2022-09-12-BiocIntro-Heidelberg/ Heidelberg Germany "Charlotte Soneson, Laurent Gatto" | ||
| "1, 8, 15, 22 June 2022" Australian BioCommons https://www.biocommons.org.au/ bioc-intro https://zenodo.org/records/6766951 Online "Saskia Freytag, Adele Barugahare, Maria Doyle, Brendan Ansell" | ||
| 2022 UCLouvain https://uclouvain.be/en/index.html bioc-intro Brussels Belgium Laurent Gatto |
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