From b696f7f8e995911f1e98d9187509051ef0dbf744 Mon Sep 17 00:00:00 2001 From: csmagnano Date: Wed, 10 Jan 2024 14:42:57 -0500 Subject: [PATCH] Changed .Rproj filename and updated README --- README.md | 112 +++++++++++--------------- FIXME.Rproj => osca-carpentries.Rproj | 0 2 files changed, 47 insertions(+), 65 deletions(-) rename FIXME.Rproj => osca-carpentries.Rproj (100%) diff --git a/README.md b/README.md index a0c1445..4d89507 100644 --- a/README.md +++ b/README.md @@ -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/ diff --git a/FIXME.Rproj b/osca-carpentries.Rproj similarity index 100% rename from FIXME.Rproj rename to osca-carpentries.Rproj