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13 changes: 12 additions & 1 deletion docs/index.html
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<div id="courses-and-guides" class="section level1 unnumbered">
<h1>Courses and Guides</h1>
<p>Please check out our full collection of AnVIL and related resources below!</p>
<p>This page was last updated on 2023-12-01 16:45:43</p>
<p>This page was last updated on 2023-12-01 17:28:46</p>
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<h2>AnVIL Resources</h2>
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<td style="text-align:left;">
<a href="https://hutchdatascience.org/AnVIL_Urban_Genomics_PCA/">AnVIL Urban Genomics: Identifying population structure among feral pigeon populations</a>
</td>
<td style="text-align:left;">
Lab module and lectures for exploring PCA using feral pigeon populations
</td>
<td style="text-align:left;">
anvil, genomics, pca, urban-data-science
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/fhdsl/AnVIL_WDLs/tree/main">AnVIL WDL Workflows</a>
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<td style="text-align:left;">
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Please check out our full collection of AnVIL and related resources below!

This page was last updated on 2023-12-01 16:45:43
This page was last updated on 2023-12-01 17:28:46

## AnVIL Resources {-}

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<td style="text-align:left;"> A guide for instructors using AnVIL for workshops, lessons, or courses. </td>
<td style="text-align:left;"> anvil, education </td>
</tr>
<tr>
<td style="text-align:left;"> [AnVIL Urban Genomics: Identifying population structure among feral pigeon populations](https://hutchdatascience.org/AnVIL_Urban_Genomics_PCA/) </td>
<td style="text-align:left;"> Lab module and lectures for exploring PCA using feral pigeon populations </td>
<td style="text-align:left;"> anvil, genomics, pca, urban-data-science </td>
</tr>
<tr>
<td style="text-align:left;"> [AnVIL WDL Workflows](https://github.com/fhdsl/AnVIL_WDLs/tree/main) </td>
<td style="text-align:left;"> Raw WDL workflow files for use on AnVIL and other platforms </td>
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[["index.html", "AnVIL Collection Courses and Guides AnVIL Resources GDSCN Resources", " AnVIL Collection Courses and Guides Please check out our full collection of AnVIL and related resources below! This page was last updated on 2023-12-01 16:45:43 AnVIL Resources Book Name Description Topics AnVIL Demos ⏱ 30-minute demos and tutorials from our live AnVIL series anvil, cloud, cloud-computing, genomics, research AnVIL Instructor Guide A guide for instructors using AnVIL for workshops, lessons, or courses. anvil, education AnVIL WDL Workflows Raw WDL workflow files for use on AnVIL and other platforms anvil, genomics, wdl, workflows AnVIL: SRA Data Pull Sequence Read Archive (SRA) data into AnVIL anvil, genomics, ncbi-database, sequence-read-archive AnVIL: Subsetting Your Data with WDL Tutorial for running the fastq_subsample WDL workflow on AnVIL! anvil, genomics, wdl, wdl-workflow, workflow Epigenetics on AnVIL: Nature vs Nurture An introductory activity for epigenetics, or the idea of \"nature versus nurture\" in genetics. Learners use the UCSC Genome Browser. anvil, course, epigenetics, human-genomes, module, ucsc-browser Getting Started on AnVIL A guide for getting started using AnVIL anvil, cloud-computing Molecular Phylogenetic Techniques A semester-long course on the basics of molecular phylogenetic techniques anvil, r-programming GDSCN Resources Book Name Description Topics GDSCN Book: SARS with Galaxy on AnVIL Lab module and lectures for variant detection in SARS-CoV-2 using Galaxy anvil, gdscn, genomics, module, sars-cov-2, variant-detection GDSCN Book: SARS with RStudio on AnVIL Lab module and lectures for identifying phylogenetic history of SARS variants using R anvil, gdscn, phylogenetic-analysis, sars-cov-2 Intro R with swirl Lab exercise: learn basic R programming through interactive swirl lessons gdscn, swirl Statistics for Genomics: Differential Expression A set of lab modules for an introduction to differential gene expression anvil, cloud-computing, gdscn, gene-expression Statistics for Genomics: PCA A set of lab modules for PCA analysis anvil, gdscn, genomics Statistics for Genomics: scRNAseq A set of lab modules for single cell RNA-seq analysis anvil, gdscn, rna-seq, scrna-seq "],["youtube-videos.html", "YouTube Videos AnVIL GDSCN", " YouTube Videos AnVIL Check out the AnVIL YouTube channel: https://www.youtube.com/@anvilproject1223 AnVIL “Shorts” (AnVIL in 2 minutes) Video Google Slides Sharing on AnVIL Go to slides AnVIL for Analysts Go to slides AnVIL for Data Submitters Go to slides Reproducibility on AnVIL Go to slides Sequence Read Archive (SRA) data on AnVIL Go to slides AnVIL for Instructors Go to slides Scalability on AnVIL Go to slides Standardization on AnVIL Go to slides Migrate your tools &amp; pipelines on AnVIL Go to slides Sharing on AnVIL for Instructors Go to slides AnVIL for Lead Investigators Go to slides Share tools &amp; pipelines on AnVIL Go to slides Discover tools &amp; pipelines on AnVIL Go to slides NIH Data Management and Sharing on AnVIL Go to slides AnVIL Getting Started Video Google Slides Why AnVIL? Go to slides Starting Jupyter on the AnVIL Platform Go to slides Starting RStudio on the AnVIL Platform Go to slides Starting Galaxy on the AnVIL Platform Go to slides Welcome to AnVIL! Portal homepage tour edition! #anvilproject #bioinformatics #cloudcomputing N/A Welcome to AnVIL! Getting Help edition! #anvilproject #bioinformatics #cloudcomputing N/A AnVIL Monthly Demos Video Google Slides AnVIL Demos: Introduction to AnVIL - 2023/03/23 N/A AnVIL Demos: Using the Human Pangenome on AnVIL - 2023/04/27 N/A AnVIL Demos: WARP Pipelines in AnVIL/Terra - 2023/05/18 N/A AnVIL Demos: How to combine data across workspaces - 06/22/2023 N/A AnVIL Demos: Interactive Genomic Data Science with Bioconductor - 07/20/2023 N/A AnVIL Demos: Running Galaxy in AnVIL - 08/31/2023 Go to slides AnVIL Demos: Epigenetics in AnVIL - 2023/09/21 Go to slides AnVIL Demo: DUOS - a tour of AnVIL’s innovative data sharing platform - 2023/10/26 N/A AnVIL WDL Book Name Description Topics none none none GDSCN Check out the GDSCN YouTube channel: https://www.youtube.com/@genomicdatasciencecommunit2514 SARS with Galaxy on AnVIL Video Google Slides Introduction to SARS-CoV-2 Variant Detection Go to slides What is a variant? Go to slides The sequencing revolution Go to slides Alignments &amp; data structure Go to slides Cloud computing Go to slides AnVIL laboratory introduction Go to slides BioDIGS Soil Project Protocols Book Name Description Topics none none none "],["contribute.html", "Contribute Courses and Guides AnVIL Shorts", " Contribute Courses and Guides What is needed to list my repository? The AnVIL Collection workflow uses three important things to add courses to the Collection. These are the repository description, homepage, and topics tags. Repositories must be set to public to be listed in the Collection. How often is the Collection updated? The collection is rendered nightly between 3am and 5am EST. How can I add my new course/content to the Collection? Your repository must be created under the jhudsl or fhdsl organizations and meet the above criteria. The repository must also have the tag anvil or gdscn. For repositories under other organizations, you can fork the repository into the jhudsl or fhdsl organizations. Example I want to use the raw Collection data! You can use the following link: https://raw.githubusercontent.com/fhdsl/AnVIL_Collection/main/resources/collection.tsv How do I edit description, homepage, and topics? Where to edit Start by clicking the gear button on the top right of the repository page on GitHub next to “About”. Where is the gear button next to the “About” menu? Edit repository description Enter a concise description, for example “A guide for instructors using AnVIL for workshops, lessons, or courses.” Add a description to the repository. Edit repository homepage Make sure you link to the website where your course is being rendered. For example, this repository links to https://jhudatascience.org/AnVIL_Book_Instructor_Guide. Add a homepage link to the repository. Edit repository topics Finally, you should add any relevant topics, as they will be listed in the Collection table! Add tags to the repository. AnVIL Shorts Make sure you add any AnVIL “Shorts” videos you create to this playlist! https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uCABkMngSYjPo_3c-nUUmio In order for Google Slides to get linked correctly, please include the link somewhere in your video description. For example, you could include text like this: You can see the slides for this video here: https://docs.google.com/presentation/d/1IOOzvnKoTMJdRLFjCup_9FqQpumP07NwoBb9mIlD7lM/edit?usp=sharing Make sure the slides are set to “Anyone with the link” is a “Viewer”. "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on our course contributors table guidelines.     Credits Names Technical Course Publishing Engineer and Maintainer Ava Hoffman Template Publishing Engineers Candace Savonen, Carrie Wright Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Candace Savonen Package Developers (ottrpal) John Muschelli, Candace Savonen, Carrie Wright "],["session-info.html", "Session Info", " Session Info ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.0.2 (2020-06-22) ## os Ubuntu 20.04.3 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2023-12-01 ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date lib source ## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.3) ## bookdown 0.24 2022-02-15 [1] Github (rstudio/bookdown@88bc4ea) ## callr 3.4.4 2020-09-07 [1] RSPM (R 4.0.2) ## cli 2.0.2 2020-02-28 [1] RSPM (R 4.0.0) ## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0) ## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3) ## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3) ## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0) ## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3) ## evaluate 0.14 2019-05-28 [1] RSPM (R 4.0.3) ## fansi 0.4.1 2020-01-08 [1] RSPM (R 4.0.0) ## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3) ## glue 1.6.1 2022-01-22 [1] CRAN (R 4.0.2) ## htmltools 0.5.0 2020-06-16 [1] RSPM (R 4.0.1) ## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2) ## knitr 1.33 2022-02-15 [1] Github (yihui/knitr@a1052d1) ## lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.2) ## magrittr 2.0.2 2022-01-26 [1] CRAN (R 4.0.2) ## memoise 1.1.0 2017-04-21 [1] RSPM (R 4.0.0) ## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2) ## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3) ## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3) ## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2) ## ps 1.3.4 2020-08-11 [1] RSPM (R 4.0.2) ## purrr 0.3.4 2020-04-17 [1] RSPM (R 4.0.3) ## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0) ## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3) ## rlang 0.4.10 2022-02-15 [1] Github (r-lib/rlang@f0c9be5) ## rmarkdown 2.10 2022-02-15 [1] Github (rstudio/rmarkdown@02d3c25) ## rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.2) ## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3) ## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3) ## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3) ## testthat 3.0.1 2022-02-15 [1] Github (R-lib/testthat@e99155a) ## usethis 2.1.5.9000 2022-02-15 [1] Github (r-lib/usethis@57b109a) ## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2) ## xfun 0.26 2022-02-15 [1] Github (yihui/xfun@74c2a66) ## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]
[["index.html", "AnVIL Collection Courses and Guides AnVIL Resources GDSCN Resources", " AnVIL Collection Courses and Guides Please check out our full collection of AnVIL and related resources below! This page was last updated on 2023-12-01 17:28:46 AnVIL Resources Book Name Description Topics AnVIL Demos ⏱ 30-minute demos and tutorials from our live AnVIL series anvil, cloud, cloud-computing, genomics, research AnVIL Instructor Guide A guide for instructors using AnVIL for workshops, lessons, or courses. anvil, education AnVIL Urban Genomics: Identifying population structure among feral pigeon populations Lab module and lectures for exploring PCA using feral pigeon populations anvil, genomics, pca, urban-data-science AnVIL WDL Workflows Raw WDL workflow files for use on AnVIL and other platforms anvil, genomics, wdl, workflows AnVIL: SRA Data Pull Sequence Read Archive (SRA) data into AnVIL anvil, genomics, ncbi-database, sequence-read-archive AnVIL: Subsetting Your Data with WDL Tutorial for running the fastq_subsample WDL workflow on AnVIL! anvil, genomics, wdl, wdl-workflow, workflow Epigenetics on AnVIL: Nature vs Nurture An introductory activity for epigenetics, or the idea of \"nature versus nurture\" in genetics. Learners use the UCSC Genome Browser. anvil, course, epigenetics, human-genomes, module, ucsc-browser Getting Started on AnVIL A guide for getting started using AnVIL anvil, cloud-computing Molecular Phylogenetic Techniques A semester-long course on the basics of molecular phylogenetic techniques anvil, r-programming GDSCN Resources Book Name Description Topics GDSCN Book: SARS with Galaxy on AnVIL Lab module and lectures for variant detection in SARS-CoV-2 using Galaxy anvil, gdscn, genomics, module, sars-cov-2, variant-detection GDSCN Book: SARS with RStudio on AnVIL Lab module and lectures for identifying phylogenetic history of SARS variants using R anvil, gdscn, phylogenetic-analysis, sars-cov-2 Intro R with swirl Lab exercise: learn basic R programming through interactive swirl lessons gdscn, swirl Statistics for Genomics: Differential Expression A set of lab modules for an introduction to differential gene expression anvil, cloud-computing, gdscn, gene-expression Statistics for Genomics: PCA A set of lab modules for PCA analysis anvil, gdscn, genomics Statistics for Genomics: scRNAseq A set of lab modules for single cell RNA-seq analysis anvil, gdscn, rna-seq, scrna-seq "],["youtube-videos.html", "YouTube Videos AnVIL GDSCN", " YouTube Videos AnVIL Check out the AnVIL YouTube channel: https://www.youtube.com/@anvilproject1223 AnVIL “Shorts” (AnVIL in 2 minutes) Video Google Slides Sharing on AnVIL Go to slides AnVIL for Analysts Go to slides AnVIL for Data Submitters Go to slides Reproducibility on AnVIL Go to slides Sequence Read Archive (SRA) data on AnVIL Go to slides AnVIL for Instructors Go to slides Scalability on AnVIL Go to slides Standardization on AnVIL Go to slides Migrate your tools &amp; pipelines on AnVIL Go to slides Sharing on AnVIL for Instructors Go to slides AnVIL for Lead Investigators Go to slides Share tools &amp; pipelines on AnVIL Go to slides Discover tools &amp; pipelines on AnVIL Go to slides NIH Data Management and Sharing on AnVIL Go to slides AnVIL Getting Started Video Google Slides Why AnVIL? Go to slides Starting Jupyter on the AnVIL Platform Go to slides Starting RStudio on the AnVIL Platform Go to slides Starting Galaxy on the AnVIL Platform Go to slides Welcome to AnVIL! Portal homepage tour edition! #anvilproject #bioinformatics #cloudcomputing N/A Welcome to AnVIL! Getting Help edition! #anvilproject #bioinformatics #cloudcomputing N/A AnVIL Monthly Demos Video Google Slides AnVIL Demos: Introduction to AnVIL - 2023/03/23 N/A AnVIL Demos: Using the Human Pangenome on AnVIL - 2023/04/27 N/A AnVIL Demos: WARP Pipelines in AnVIL/Terra - 2023/05/18 N/A AnVIL Demos: How to combine data across workspaces - 06/22/2023 N/A AnVIL Demos: Interactive Genomic Data Science with Bioconductor - 07/20/2023 N/A AnVIL Demos: Running Galaxy in AnVIL - 08/31/2023 Go to slides AnVIL Demos: Epigenetics in AnVIL - 2023/09/21 Go to slides AnVIL Demo: DUOS - a tour of AnVIL’s innovative data sharing platform - 2023/10/26 N/A AnVIL WDL Book Name Description Topics none none none GDSCN Check out the GDSCN YouTube channel: https://www.youtube.com/@genomicdatasciencecommunit2514 SARS with Galaxy on AnVIL Video Google Slides Introduction to SARS-CoV-2 Variant Detection Go to slides What is a variant? Go to slides The sequencing revolution Go to slides Alignments &amp; data structure Go to slides Cloud computing Go to slides AnVIL laboratory introduction Go to slides BioDIGS Soil Project Protocols Book Name Description Topics none none none "],["contribute.html", "Contribute Courses and Guides AnVIL Shorts", " Contribute Courses and Guides What is needed to list my repository? The AnVIL Collection workflow uses three important things to add courses to the Collection. These are the repository description, homepage, and topics tags. Repositories must be set to public to be listed in the Collection. How often is the Collection updated? The collection is rendered nightly between 3am and 5am EST. How can I add my new course/content to the Collection? Your repository must be created under the jhudsl or fhdsl organizations and meet the above criteria. The repository must also have the tag anvil or gdscn. For repositories under other organizations, you can fork the repository into the jhudsl or fhdsl organizations. Example I want to use the raw Collection data! You can use the following link: https://raw.githubusercontent.com/fhdsl/AnVIL_Collection/main/resources/collection.tsv How do I edit description, homepage, and topics? Where to edit Start by clicking the gear button on the top right of the repository page on GitHub next to “About”. Where is the gear button next to the “About” menu? Edit repository description Enter a concise description, for example “A guide for instructors using AnVIL for workshops, lessons, or courses.” Add a description to the repository. Edit repository homepage Make sure you link to the website where your course is being rendered. For example, this repository links to https://jhudatascience.org/AnVIL_Book_Instructor_Guide. Add a homepage link to the repository. Edit repository topics Finally, you should add any relevant topics, as they will be listed in the Collection table! Add tags to the repository. AnVIL Shorts Make sure you add any AnVIL “Shorts” videos you create to this playlist! https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uCABkMngSYjPo_3c-nUUmio In order for Google Slides to get linked correctly, please include the link somewhere in your video description. For example, you could include text like this: You can see the slides for this video here: https://docs.google.com/presentation/d/1IOOzvnKoTMJdRLFjCup_9FqQpumP07NwoBb9mIlD7lM/edit?usp=sharing Make sure the slides are set to “Anyone with the link” is a “Viewer”. "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on our course contributors table guidelines.     Credits Names Technical Course Publishing Engineer and Maintainer Ava Hoffman Template Publishing Engineers Candace Savonen, Carrie Wright Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Candace Savonen Package Developers (ottrpal) John Muschelli, Candace Savonen, Carrie Wright "],["session-info.html", "Session Info", " Session Info ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.0.2 (2020-06-22) ## os Ubuntu 20.04.3 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2023-12-01 ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date lib source ## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.3) ## bookdown 0.24 2022-02-15 [1] Github (rstudio/bookdown@88bc4ea) ## callr 3.4.4 2020-09-07 [1] RSPM (R 4.0.2) ## cli 2.0.2 2020-02-28 [1] RSPM (R 4.0.0) ## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0) ## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3) ## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3) ## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0) ## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3) ## evaluate 0.14 2019-05-28 [1] RSPM (R 4.0.3) ## fansi 0.4.1 2020-01-08 [1] RSPM (R 4.0.0) ## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3) ## glue 1.6.1 2022-01-22 [1] CRAN (R 4.0.2) ## htmltools 0.5.0 2020-06-16 [1] RSPM (R 4.0.1) ## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2) ## knitr 1.33 2022-02-15 [1] Github (yihui/knitr@a1052d1) ## lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.2) ## magrittr 2.0.2 2022-01-26 [1] CRAN (R 4.0.2) ## memoise 1.1.0 2017-04-21 [1] RSPM (R 4.0.0) ## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2) ## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3) ## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3) ## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2) ## ps 1.3.4 2020-08-11 [1] RSPM (R 4.0.2) ## purrr 0.3.4 2020-04-17 [1] RSPM (R 4.0.3) ## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0) ## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3) ## rlang 0.4.10 2022-02-15 [1] Github (r-lib/rlang@f0c9be5) ## rmarkdown 2.10 2022-02-15 [1] Github (rstudio/rmarkdown@02d3c25) ## rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.2) ## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3) ## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3) ## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3) ## testthat 3.0.1 2022-02-15 [1] Github (R-lib/testthat@e99155a) ## usethis 2.1.5.9000 2022-02-15 [1] Github (r-lib/usethis@57b109a) ## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2) ## xfun 0.26 2022-02-15 [1] Github (yihui/xfun@74c2a66) ## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]

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