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docs/Session-info.md

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docs/index.html

@@ -133,7 +133,7 @@ <h1 class="title">AnVIL Collection</h1>
 <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 2023-06-28 03:14:46</p>
+<p>This page was last updated on 2023-06-29 03:12:23</p>
 <div id="anvil-resources" class="section level2 unnumbered">
 <h2>AnVIL Resources</h2>
 <table>

docs/index.md

@@ -13,7 +13,7 @@ favicon: assets/AnVIL_style/anvil_favicon.ico
 
 Please check out our full collection of AnVIL and related resources below!
 
-This page was last updated on 2023-06-28 03:14:46
+This page was last updated on 2023-06-29 03:12:23
 
 ## AnVIL Resources {-}
 

docs/search_index.json

@@ -1 +1 @@
-[["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 2023-06-28 03:14:46 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: SRA Data Pull Sequence Read Archive (SRA) data into AnVIL anvil, genomics, ncbi-database, sequence-read-archive 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 "],["contribute.html", "Contribute 0.1 What is needed to list my repository? 0.2 How often is the Collection updated? 0.3 How can I add my new course/content to the Collection? 0.4 I want to use the raw Collection data! 0.5 How do I edit description, homepage, and topics?", " Contribute 0.1 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. 0.2 How often is the Collection updated? The collection is rendered nightly between 3am and 5am EST. 0.3 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 0.4 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 0.5 How do I edit description, homepage, and topics? 0.5.1 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? 0.5.2 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. 0.5.3 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. 0.5.4 Edit repository topics Finally, you should add any relevant topics, as they will be listed in the Collection table! Add tags to the repository. "],["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 2023-06-28 ## ## ─ 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 2023-06-29 03:12:23 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: SRA Data Pull Sequence Read Archive (SRA) data into AnVIL anvil, genomics, ncbi-database, sequence-read-archive 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 "],["contribute.html", "Contribute 0.1 What is needed to list my repository? 0.2 How often is the Collection updated? 0.3 How can I add my new course/content to the Collection? 0.4 I want to use the raw Collection data! 0.5 How do I edit description, homepage, and topics?", " Contribute 0.1 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. 0.2 How often is the Collection updated? The collection is rendered nightly between 3am and 5am EST. 0.3 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 0.4 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 0.5 How do I edit description, homepage, and topics? 0.5.1 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? 0.5.2 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. 0.5.3 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. 0.5.4 Edit repository topics Finally, you should add any relevant topics, as they will be listed in the Collection table! Add tags to the repository. "],["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 2023-06-29 ## ## ─ 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. "]]

docs/session-info.html

@@ -139,7 +139,7 @@ <h1>Session Info</h1>
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2023-06-28                  
+##  date     2023-06-29                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version    date       lib source