|
9 | 9 | <img style="height:100px;" alt="tidybulk" src="https://github.com/Bioconductor/BiocStickers/blob/master/tidybulk/tidybulk.png?raw=true"/> |
10 | 10 | </p> |
11 | 11 |
|
12 | | -## Instructor names and contact information |
| 12 | +## Workshop Description |
13 | 13 |
|
14 | | -* Maria Doyle <Maria.Doyle at petermac.org> |
15 | | -* Stefano Mangiola <mangiola.s at wehi.edu.au> |
| 14 | +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. |
16 | 15 |
|
17 | | -## Syllabus |
| 16 | +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/). |
| 17 | + |
| 18 | +### Pre-requisites |
| 19 | + |
| 20 | +* Basic familiarity with single-cell transcriptomic analyses |
| 21 | +* Basic familiarity with tidyverse |
| 22 | + |
| 23 | +## Workshop goals |
18 | 24 |
|
19 | | -Material [web page](https://tidytranscriptomics-workshops.github.io/bioc2022_tidytranscriptomics/articles/tidytranscriptomics_case_study.html). |
| 25 | +* To approach single-cell data representation and analysis though a tidy data paradigm, integrating tidyverse with tidySingleCellExperiment. |
| 26 | +* Compare SingleCellExperiment and tidy representation |
| 27 | +* Apply tidy functions to SingleCellExperiment objects |
| 28 | +* Reproduce a real-world case study that showcases the power of tidy single-cell methods |
20 | 29 |
|
21 | | -More details on the workshop are below. |
| 30 | +### What you will learn |
| 31 | + |
| 32 | +* Basic tidy operations possible with tidySingleCellExperiment |
| 33 | +* The differences between SingleCellExperiment representation and tidy representation |
| 34 | +* How to interface SingleCellExperiment with tidy manipulation and visualisation |
| 35 | +* A real-world case study that will showcase the power of tidy single-cell methods compared with base/ad-hoc methods |
| 36 | + |
| 37 | +### What you will not learn |
| 38 | + |
| 39 | +* The molecular technology of single-cell sequencing |
| 40 | +* The fundamentals of single-cell data analysis |
| 41 | +* The fundamentals of tidy data analysis |
| 42 | + |
| 43 | +### Workshop Participation |
| 44 | + |
| 45 | +The workshop format is a 1.5 hour session consisting of hands-on demos, exercises and Q&A. |
| 46 | + |
| 47 | +## Syllabus |
| 48 | + |
| 49 | +Material [web page](https://tidytranscriptomics-workshops.github.io/bioc2022_tidytranscriptomics/articles/tidytranscriptomics_case_study.html). More details on the workshop are below. |
22 | 50 |
|
23 | 51 | ## Workshop package installation |
24 | 52 |
|
@@ -63,46 +91,8 @@ browseVignettes("bioc2022tidytranscriptomics") |
63 | 91 |
|
64 | 92 | 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. |
65 | 93 |
|
66 | | -## Workshop Description |
67 | | - |
68 | | -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. |
69 | | - |
70 | | -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/). |
71 | | - |
72 | | -### Pre-requisites |
73 | | - |
74 | | -* Basic familiarity with single-cell transcriptomic analyses |
75 | | -* Basic familiarity with tidyverse |
76 | | - |
77 | | - |
78 | | -### Workshop Participation |
79 | | - |
80 | | -The workshop format is a 1.5 hour session consisting of hands-on demos, exercises and Q&A. |
81 | | - |
82 | | - |
83 | | -## Workshop goals and objectives |
84 | | - |
85 | | -### Learning goals |
86 | | - |
87 | | -* To approach single-cell data representation and analysis though a tidy data paradigm, integrating tidyverse with tidySingleCellExperiment. |
88 | | - |
89 | | - |
90 | | -### Learning objectives |
91 | | - |
92 | | -* Compare SingleCellExperiment and tidy representation |
93 | | -* Apply tidy functions to SingleCellExperiment objects |
94 | | -* Reproduce a real-world case study that showcases the power of tidy single-cell methods |
95 | | - |
96 | | - |
97 | | -### What you will learn |
98 | | - |
99 | | -* Basic tidy operations possible with tidySingleCellExperiment |
100 | | -* The differences between SingleCellExperiment representation and tidy representation |
101 | | -* How to interface SingleCellExperiment with tidy manipulation and visualisation |
102 | | -* A real-world case study that will showcase the power of tidy single-cell methods compared with base/ad-hoc methods |
| 94 | +## Instructor names and contact information |
103 | 95 |
|
104 | | -### What you will not learn |
| 96 | +* Maria Doyle <Maria.Doyle at petermac.org> |
| 97 | +* Stefano Mangiola <mangiola.s at wehi.edu.au> |
105 | 98 |
|
106 | | -* The molecular technology of single-cell sequencing |
107 | | -* The fundamentals of single-cell data analysis |
108 | | -* The fundamentals of tidy data analysis |
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