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mblue9 authored Jun 7, 2022
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<img style="height:100px;" alt="tidybulk" src="https://github.com/Bioconductor/BiocStickers/blob/master/tidybulk/tidybulk.png?raw=true"/>
</p>

## Instructor names and contact information
## Workshop Description

* Maria Doyle <Maria.Doyle at petermac.org>
* Stefano Mangiola <mangiola.s at wehi.edu.au>
This tutorial will present how to perform analysis of single-cell RNA sequencing data following the tidy data paradigm. The tidy data paradigm provides a standard way to organise data values within a dataset, where each variable is a column, each observation is a row, and data is manipulated using an easy-to-understand vocabulary. Most importantly, the data structure remains consistent across manipulation and analysis functions.

## Syllabus
This can be achieved with the integration of packages present in the R CRAN and Bioconductor ecosystem, including [tidySingleCellExperiment](https://stemangiola.github.io/tidySingleCellExperiment/) and [tidyverse](https://www.tidyverse.org/). These packages are part of the tidytranscriptomics suite that introduces a tidy approach to RNA sequencing data representation and analysis. For more information see the [tidy transcriptomics blog](https://stemangiola.github.io/tidytranscriptomics/).

### Pre-requisites

* Basic familiarity with single-cell transcriptomic analyses
* Basic familiarity with tidyverse

## Workshop goals

Material [web page](https://tidytranscriptomics-workshops.github.io/bioc2022_tidytranscriptomics/articles/tidytranscriptomics_case_study.html).
* To approach single-cell data representation and analysis though a tidy data paradigm, integrating tidyverse with tidySingleCellExperiment.
* Compare SingleCellExperiment and tidy representation
* Apply tidy functions to SingleCellExperiment objects
* Reproduce a real-world case study that showcases the power of tidy single-cell methods

More details on the workshop are below.
### What you will learn

* Basic tidy operations possible with tidySingleCellExperiment
* The differences between SingleCellExperiment representation and tidy representation
* How to interface SingleCellExperiment with tidy manipulation and visualisation
* A real-world case study that will showcase the power of tidy single-cell methods compared with base/ad-hoc methods

### What you will not learn

* The molecular technology of single-cell sequencing
* The fundamentals of single-cell data analysis
* The fundamentals of tidy data analysis

### Workshop Participation

The workshop format is a 1.5 hour session consisting of hands-on demos, exercises and Q&A.

## Syllabus

Material [web page](https://tidytranscriptomics-workshops.github.io/bioc2022_tidytranscriptomics/articles/tidytranscriptomics_case_study.html). More details on the workshop are below.

## Workshop package installation

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To run the code, you could then copy and paste the code from the workshop vignette or [R markdown file](https://raw.githubusercontent.com/tidytranscriptomics-workshops/bioc2022_tidytranscriptomics/master/vignettes/tidytranscriptomics.Rmd) into a new R Markdown file on your computer.

## Workshop Description

This tutorial will present how to perform analysis of single-cell RNA sequencing data following the tidy data paradigm. The tidy data paradigm provides a standard way to organise data values within a dataset, where each variable is a column, each observation is a row, and data is manipulated using an easy-to-understand vocabulary. Most importantly, the data structure remains consistent across manipulation and analysis functions.

This can be achieved with the integration of packages present in the R CRAN and Bioconductor ecosystem, including [tidySingleCellExperiment](https://stemangiola.github.io/tidySingleCellExperiment/) and [tidyverse](https://www.tidyverse.org/). These packages are part of the tidytranscriptomics suite that introduces a tidy approach to RNA sequencing data representation and analysis. For more information see the [tidy transcriptomics blog](https://stemangiola.github.io/tidytranscriptomics/).

### Pre-requisites

* Basic familiarity with single-cell transcriptomic analyses
* Basic familiarity with tidyverse


### Workshop Participation

The workshop format is a 1.5 hour session consisting of hands-on demos, exercises and Q&A.


## Workshop goals and objectives

### Learning goals

* To approach single-cell data representation and analysis though a tidy data paradigm, integrating tidyverse with tidySingleCellExperiment.


### Learning objectives

* Compare SingleCellExperiment and tidy representation
* Apply tidy functions to SingleCellExperiment objects
* Reproduce a real-world case study that showcases the power of tidy single-cell methods


### What you will learn

* Basic tidy operations possible with tidySingleCellExperiment
* The differences between SingleCellExperiment representation and tidy representation
* How to interface SingleCellExperiment with tidy manipulation and visualisation
* A real-world case study that will showcase the power of tidy single-cell methods compared with base/ad-hoc methods
## Instructor names and contact information

### What you will not learn
* Maria Doyle <Maria.Doyle at petermac.org>
* Stefano Mangiola <mangiola.s at wehi.edu.au>

* The molecular technology of single-cell sequencing
* The fundamentals of single-cell data analysis
* The fundamentals of tidy data analysis

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