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https://github.com/bodenmillergroup/demos
Repository containing demonstrations of lab software
https://github.com/bodenmillergroup/demos
bioconductor demo
Last synced: 7 days ago
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Repository containing demonstrations of lab software
- Host: GitHub
- URL: https://github.com/bodenmillergroup/demos
- Owner: BodenmillerGroup
- Created: 2021-06-05T18:00:26.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2023-09-14T08:44:55.000Z (about 1 year ago)
- Last Synced: 2024-05-17T00:09:43.493Z (6 months ago)
- Topics: bioconductor, demo
- Homepage: https://bodenmillergroup.github.io/demos
- Size: 118 MB
- Stars: 5
- Watchers: 6
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Software demonstrations
This repository contains software demonstrations of the Bodenmiller laboratory.
## Structure
Each demo is hosted in its independent branch.
The most current demonstration is compiled as `index.html` in the `docs` folder and will automatically be hosted at [bodenmillergroup.github.io/demos](https://www.bodenmillergroup.github.io/demos)
The following demos are gathered here:
### EuroBioc2023 workshop presentation
The workshop given at the [EuroBioc2023](https://eurobioc2023.bioconductor.org/) conference can be found [here](https://bodenmillergroup.github.io/demos/).
It highlights the use of the [cytoviewer](https://www.bioconductor.org/packages/release/bioc/html/cytoviewer.html) and [cytomapper](https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html) R/Bioconductor packages for multiplexed image data visualization in R.
To follow along, please clone the repository
```
git clone https://github.com/BodenmillerGroup/demos.git
```
and open the `EuroBioc2023_workshop.Rmd` file.
### EuroBioc2022 workshop presentation
The workshop given at the [EuroBioc2022](https://eurobioc2022.bioconductor.org/) conference can be found [here](https://github.com/BodenmillerGroup/demos/blob/EuroBioc2022/docs/EuroBioc2022_workshop.Rmd).
It highlights the use of the [imcRtools](https://www.bioconductor.org/packages/release/bioc/html/imcRtools.html) R/Bioconductor package for spatial data analysis and visualization.
To follow along, please clone the repository
```
git clone --single-branch --branch EuroBioc2022 https://github.com/BodenmillerGroup/demos.git
```
and open the `EuroBioc2022_workshop.Rmd` file under `docs`.
### Bioc2022 workshop presentation
The workshop given at the [Bioc2022](https://bioc2022.bioconductor.org/) conference can be found [here](https://github.com/BodenmillerGroup/demos/blob/Bioc2022/docs/Bioc2022_workshop.Rmd).
It highlights the use of the [steinbock](https://github.com/BodenmillerGroup/steinbock) python framework and the [imcRtools](https://www.bioconductor.org/packages/release/bioc/html/imcRtools.html) R/Bioconductor package.
To follow along, please clone the repository
```
git clone --single-branch --branch Bioc2022 https://github.com/BodenmillerGroup/demos.git
```
and open the `Bioc2022_workshop.Rmd` file under `docs`.
### Bioc2021 workshop presentation
The workshop given at the [Bioc2021](https://bioc2021.bioconductor.org/) conference can be found [here](https://github.com/BodenmillerGroup/demos/blob/Bioc2021/docs/Bioc2021_workshop.Rmd).
It highlights the use of the [cytomapper](https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html) package.
### useR! 2021 presentation
The [cytomapper](https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html) demonstration as presented at the [useR! 2021 conference](https://user2021.r-project.org/) can be found [here](https://github.com/BodenmillerGroup/demos/blob/useR2021/docs/index.Rmd).
The presentation is hosted at [https://nilseling.github.io/useR2021_cytomapper](https://nilseling.github.io/useR2021_cytomapper)
### Indiana O’Brien Center Microscopy Workshop
The [Indiana O’Brien Center Microscopy Workshop](http://static.medicine.iupui.edu/obrien/2021Schedule.pdf) on the [cytomapper](https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html) package was hosted between 7th and 10th June 2021.
All resources for the demonstration can be found [here](https://github.com/BodenmillerGroup/demos/tree/IndianaOBrienCentre).
Please follow the [analysis script](https://github.com/BodenmillerGroup/demos/blob/IndianaOBrienCentre/scripts/cytomapper_workshop.Rmd) to reproduce the presented demo.
## Maintainer
[Nils Eling](https://github.com/nilseling)
## Contributor
[Lasse Meyer](https://github.com/lassedochreden)