generated from carpentries/workbench-template-rmd
-
-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Changed .Rproj filename and updated README
- Loading branch information
Showing
2 changed files
with
47 additions
and
65 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,74 +1,56 @@ | ||
| # The Carpentries Workbench Template R Markdown Lesson | ||
| # Orchestrating Single-Cell Analysis with Bioconductor | ||
|
|
||
| This lesson is a template lesson that uses [The Carpentries Workbench][workbench]. | ||
| This is a pre-alpha adaptation of the 2023 ISMB OSCA tutorial using The Carpentries Workbench lesson template. | ||
|
|
||
| ## Note about lesson life cycle stage | ||
| Although the `config.yaml` states the life cycle stage as pre-alpha, **the template is stable and ready to use**. The life cycle stage is preset to `"pre-alpha"` as this setting is appropriate for new lessons initialised using the template. | ||
| ### Vignettes converted | ||
|
|
||
| ## Create a new repository from this template | ||
| As individual vignettes are converted into lessons, they can be added to `config.yaml` to be rendered and shown in the final Github Pages lesson. | ||
|
|
||
| To use this template to start a new lesson repository, | ||
| make sure you're logged into Github. | ||
| Visit https://github.com/carpentries/workbench-template-rmd/generate | ||
| and follow the instructions. | ||
| Checking the 'Include all branches' option will save some time waiting for the first website build | ||
| when your new repository is initialised. | ||
| ### Vignettes not yet converted | ||
| - Introduction to Bioconductor | ||
| - Exploratory data analysis | ||
| - Cell type annotation | ||
| - Multi-sample analyses | ||
| - Working with large data | ||
| - Accessing data from the Human Cell Atlas | ||
|
|
||
| If you have any questions, contact [@tobyhodges](https://github.com/tobyhodges) | ||
| ## Description | ||
|
|
||
| ## Configure a new lesson | ||
| In the last few years, the profiling of a large number of genome-wide features | ||
| in individual cells has become routine. Consequently, a plethora of tools for | ||
| the analysis of single-cell data has been developed, making it hard to understand | ||
| the critical steps in the analysis workflow and the best methods for each objective | ||
| of one’s study. | ||
|
|
||
| Follow the steps below to | ||
| complete the initial configuration of a new lesson repository built from this template: | ||
| This tutorial aims to provide a solid foundation in using Bioconductor tools | ||
| for single-cell RNA-seq analysis by walking through various steps of typical | ||
| workflows using example datasets. | ||
|
|
||
| 1. **Make sure GitHub Pages is activated:** | ||
| navigate to _Settings_, | ||
| select _Pages_ from the left sidebar, | ||
| and make sure that `gh-pages` is selected as the branch to build from. | ||
| If no `gh-pages` branch is available, check _Actions_ to see if the first | ||
| website build workflows are still running. | ||
| The branch should become available when those have completed. | ||
| 1. **Adjust the `config.yaml` file:** | ||
| this file contains global parameters for your lesson site. | ||
| Individual fields within the file are documented with comments (beginning with `#`) | ||
| At minimum, you should adjust all the fields marked 'FIXME': | ||
| - `title` | ||
| - `created` | ||
| - `keywords` | ||
| - `life_cycle` (the default, _pre-alpha_, is the appropriate for brand new lessons) | ||
| - `contact` | ||
| 1. **Annotate the repository** with site URL and topic tags: | ||
| navigate back to the repository landing page and | ||
| click on the gear wheel/cog icon (similar to ⚙️) | ||
| at the top-right of the _About_ box. | ||
| Check the "Use your GitHub Pages website" option, | ||
| and [add some keywords and other annotations to describe your lesson](https://cdh.carpentries.org/the-carpentries-incubator.html#topic-tags) | ||
| in the _Topics_ field. | ||
| At minimum, these should include: | ||
| - `lesson` | ||
| - the life cycle of the lesson (e.g. `pre-alpha`) | ||
| - the human language the lesson is written in (e.g. `deutsch`) | ||
| 1. **Adjust the name of the `.Rproj` file.** | ||
| It is simplest to make this match the name of the repository. | ||
| 1. **Adjust the | ||
| `CODE_OF_CONDUCT.md`, `CONTRIBUTING.md`, and `LICENSE.md` files** | ||
| as appropriate for your project. | ||
| - `CODE_OF_CONDUCT.md`: | ||
| if you are using this template for a project outside The Carpentries, | ||
| you should adjust this file to describe | ||
| who should be contacted with Code of Conduct reports, | ||
| and how those reports will be handled. | ||
| - `CONTRIBUTING.md`: | ||
| depending on the current state and maturity of your project, | ||
| the contents of the template Contributing Guide may not be appropriate. | ||
| You should adjust the file to help guide contributors on how best | ||
| to get involved and make an impact on your lesson. | ||
| - `LICENSE.md`: | ||
| in line with the terms of the CC-BY license, | ||
| you should ensure that the copyright information | ||
| provided in the license file is accurate for your project. | ||
| 1. **Update this README with | ||
| [relevant information about your lesson](https://carpentries.github.io/lesson-development-training/collaborating-newcomers.html#readme)** | ||
| and delete this section. | ||
| This tutorial uses as a "text-book" the online book "Orchestrating Single-Cell | ||
| Analysis with Bioconductor" | ||
| ([OSCA](https://bioconductor.org/books/release/OSCA/)), | ||
| started in 2018 and continuously updated by many contributors from the Bioconductor | ||
| community. Like the book, this tutorial strives to be of interest to the | ||
| experimental biologists wanting to analyze their data and to the bioinformaticians | ||
| approaching single-cell data. | ||
|
|
||
| ## Learning objectives | ||
|
|
||
| Attendees will learn how to analyze multi-condition single-cell RNA-seq from | ||
| raw data to statistical analyses and result interpretation. Students will learn | ||
| where the critical steps and methods choices are and will be able to leverage | ||
| large-data resources to analyze datasets comprising millions of cells. | ||
|
|
||
| In particular, participants will learn: | ||
|
|
||
| * How to access publicly available data, such as those from the Human Cell Atlas. | ||
| * How to perform data exploration, normalization, and dimensionality reduction. | ||
| * How to identify cell types/states and marker genes. | ||
| * How to correct for batch effects and integrate multiple samples. | ||
| * How to perform differential expression and differential abundance analysis between conditions. | ||
| * How to work with large out-of-memory datasets. | ||
|
|
||
| ## Source | ||
|
|
||
| This lesson is a template lesson that uses [The Carpentries Workbench][workbench] and is based on materials from the [OSCA tutorial at the ISMB 2023](https://bioconductor.github.io/ISMB.OSCA/). | ||
|
|
||
| [workbench]: https://carpentries.github.io/sandpaper-docs/ |
File renamed without changes.