diff --git a/index.md b/index.md index 6cfa38b1..02e1aa08 100644 --- a/index.md +++ b/index.md @@ -1,6 +1,5 @@ --- site: sandpaper::sandpaper_site -base_url: gwu-libraries.github.io --- Data Carpentry's aim is to teach researchers basic concepts, skills, and tools for working @@ -52,16 +51,16 @@ More information about this data is available on the [Data page](https://datacar | Lesson | Overview | | ----------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------ | -| [Project organization and management](https://{{page.base_url}}/organization-genomics/) | Learn how to structure your metadata, organize and document your genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database. | -| [Introduction to the command line](https://{{page.base_url}}/shell-genomics/) | Learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards. | -| [Data wrangling and processing](https://{{page.base_url}}/wrangling-genomics/) | Use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation. | -| [Introduction to cloud computing for genomics](https://{{page.base_url}}/cloud-genomics/) | Learn how to work with Amazon AWS cloud computing and how to transfer data between your local computer and cloud resources. | +| [Project organization and management](https://gwu-libraries.github.io/organization-genomics/) | Learn how to structure your metadata, organize and document your genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database. | +| [Introduction to the command line](https://gwu-libraries.github.io/shell-genomics/) | Learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards. | +| [Data wrangling and processing](https://gwu-libraries.github.io/wrangling-genomics/) | Use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation. | +| [Introduction to cloud computing for genomics](https://gwu-libraries.github.io/cloud-genomics/) | Learn how to work with Amazon AWS cloud computing and how to transfer data between your local computer and cloud resources. | # Optional Additional Lessons | Lesson | Overview | | ----------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------ | -| [Intro to R and RStudio for Genomics](https://{{page.base_url}}/genomics-r-intro/) | Use R to analyze and visualize between-sample variation. | +| [Intro to R and RStudio for Genomics](https://gwu-libraries.github.io/genomics-r-intro/) | Use R to analyze and visualize between-sample variation. | # Teaching Platform @@ -73,21 +72,21 @@ If you want to run your own instance of the server used for this workshop, follo ### Schedule A (2 days OR 4 half days) -- Half-day 1: [Project organization and management](https://datacarpentry.github.io/organization-genomics/) \& [Introduction to the command line](https://datacarpentry.github.io/shell-genomics/) -- Half-day 2: [Introduction to the command line](https://datacarpentry.github.io/shell-genomics/) (continued). -- Half-day 3 \& 4 : [Data wrangling and processing](https://datacarpentry.github.io/wrangling-genomics/) +- Half-day 1: [Project organization and management](https://gwu-libraries.github.io/organization-genomics/) \& [Introduction to the command line](https://gwu-libraries.github.io/shell-genomics/) +- Half-day 2: [Introduction to the command line](https://gwu-libraries.github.io/shell-genomics/) (continued). +- Half-day 3 \& 4 : [Data wrangling and processing](https://gwu-libraries.github.io/wrangling-genomics/) ### Schedule B (2 days OR 4 half days) -- Half-day 1: [Project organization and management](https://datacarpentry.github.io/organization-genomics/) \& [Introduction to the command line](https://datacarpentry.github.io/shell-genomics/) -- Half-day 2: [Introduction to the command line](https://datacarpentry.github.io/shell-genomics/) (continued) -- Half-day 3 \& 4: [Intro to R and RStudio for Genomics](https://datacarpentry.org/genomics-r-intro/) +- Half-day 1: [Project organization and management](https://gwu-libraries.github.io/organization-genomics/) \& [Introduction to the command line](https://gwu-libraries.github.io/shell-genomics/) +- Half-day 2: [Introduction to the command line](https://gwu-libraries.github.io/shell-genomics/) (continued) +- Half-day 3 \& 4: [Intro to R and RStudio for Genomics](https://gwu-libraries.github.io/genomics-r-intro/) ### Schedule C (3 days OR 6 half days) -- Half-day 1: [Project organization and management](https://datacarpentry.github.io/organization-genomics/) \& [Introduction to the command line](https://datacarpentry.github.io/shell-genomics/) -- Half-day 2: [Introduction to the command line](https://datacarpentry.github.io/shell-genomics/) (continued) -- Half-day 3 \& 4 : [Data wrangling and processing](https://datacarpentry.github.io/wrangling-genomics/) -- Half-day 5 \& 6: [Intro to R and RStudio for Genomics](https://datacarpentry.org/genomics-r-intro/) +- Half-day 1: [Project organization and management](https://gwu-libraries.github.io/organization-genomics/) \& [Introduction to the command line](https://gwu-libraries.github.io/shell-genomics/) +- Half-day 2: [Introduction to the command line](https://gwu-libraries.github.io/shell-genomics/) (continued) +- Half-day 3 \& 4 : [Data wrangling and processing](https://gwu-libraries.github.io/wrangling-genomics/) +- Half-day 5 \& 6: [Intro to R and RStudio for Genomics](https://gwu-libraries.github.io/genomics-r-intro/)