diff --git a/404.html b/404.html index 8cb4bc3..5832334 100644 --- a/404.html +++ b/404.html @@ -14,7 +14,7 @@
Homepage for `dms-vep-pipeline-3` test example

404

PAGE NOT FOUND

But if you don't change your direction, and if you keep looking, you may end up where you are heading.
Take me home

Copyright © 2024-present Will Hannon and Jesse Bloom

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themeConfig: {

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Homepage for `dms-vep-pipeline-3` test example

Antibody Escape ​

Here's what a page with antibody escape data might look like.

Individual Antibody Selections ​

You can include links to the antibody escape data created automatically by the dms-vep-pipeline.

You do this using normal markdown syntax with one exception – you include {target="_self"} after the link:

bash
- [LibA-220210-REGN10933-1](notebooks/fit_escape_antibody_escape_LibA-220210-REGN10933-1.html){target="_self"}

This approach will work for any file that's ordinarily present in the docs/ directory created by the pipeline. For example, .html files that contain Altair plots.

If you prefer, you can include Altair plots directly on the page.

Effects of mutations on antibody neutralization by REGN10933

You do this using a custom html-like syntax.

bash
<Figure caption="Effects of mutations on antibody neutralization by REGN10933">
     <Altair :showShadow="true" :spec-url="'htmls/REGN10933_mut_effect.html'"></Altair>
 </Figure>

The code above creates the Altair plot using the <Altair></Altair> tag and adds a figure caption with the surrounding <Figure></Figure> tag.

Copyright © 2024-present Will Hannon and Jesse Bloom

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Homepage for `dms-vep-pipeline-3` test example

Cell Entry ​

Here's what a page with functional selection data might look like.

Mutation effects on ACE2-mediated cell entry ​

Effects of mutations on ACE2 entry in HEK 293T cells

Latent phenotype mutation effects on ACE2-mediated cell entry ​

Latent phenotype of mutations effects on ACE2 entry in HEK 293T cells

Copyright © 2024-present Will Hannon and Jesse Bloom

- + \ No newline at end of file diff --git a/hashmap.json b/hashmap.json index d3cc7f2..4c5f917 100644 --- a/hashmap.json +++ b/hashmap.json @@ -1 +1 @@ -{"index.md":"D6RkxFU1","pipeline_information.md":"ClK1L7S4","antibody_escape.md":"CRI4WYeg","readme.md":"D1fUHbGs","cell_entry.md":"Cy5O-9mK"} +{"antibody_escape.md":"CRI4WYeg","pipeline_information.md":"ClK1L7S4","index.md":"D6RkxFU1","readme.md":"D1fUHbGs","cell_entry.md":"Cy5O-9mK"} diff --git a/index.html b/index.html index ce90062..ed08a9c 100644 --- a/index.html +++ b/index.html @@ -17,7 +17,7 @@
Homepage for `dms-vep-pipeline-3` test example

`dms-vep-pipeline-3` test example

A collection of data, figures, and information for `dms-vep-pipeline-3` test example

Antibody Escape

Example link to antibody escape data

Cell Entry

Example link to functional selection data

Pipeline Information

Example page detailing computational pipeline

This is the fancy homepage made with VitePress ​

Building this homepage requires some manual customization of the Markdown files in the ./homepage subdirectory of your repo. See the instructions on building a VitePress homepage for more details.

To see the less fancy documentation automatically build by the pipeline, see the Appendix.

Copyright © 2024-present Will Hannon and Jesse Bloom

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Homepage for `dms-vep-pipeline-3` test example

Pipeline Information ​

Here's an example of what an overview of the analysis pipeline could look like.

Snakemake Workflow ​

You can include a link to the repository and key data files here. You can also point to the 'Appendix' with details about the pipeline. The 'Appendix' is the same as the original docs/ created by the Snakemake pipeline.

In principle, you could also include an image of the workflow.

Copyright © 2024-present Will Hannon and Jesse Bloom

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