https://github.com/tnaake/apoptosisquantification
https://github.com/tnaake/apoptosisquantification
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/tnaake/apoptosisquantification
- Owner: tnaake
- Created: 2022-01-26T08:11:27.000Z (over 3 years ago)
- Default Branch: devel
- Last Pushed: 2023-03-14T15:31:06.000Z (over 2 years ago)
- Last Synced: 2023-12-13T03:50:31.058Z (over 1 year ago)
- Language: R
- Size: 8 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# apoptosisQuantification
The package `apoptosisQuantification` quantifies apoptosis and necroptosis
using predefined markers in proteomics datasets.
## Installation
To install the package, enter
```
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("tnaake/apoptosisQuantification")
```
## Methods to quantify apoptosis/necroptosis
The package contains three ways to quantify apoptosis/necroptosis:
1. by comparing the distribution of marker loadings and non-marker
loadings (from PCA),
2. by looking at the contribution of mitochrondrial proteins
(this might be misleading when looking at a proteomics data set),
3. by running `decoupleR` and calculating a score for
apoptosis/necroptosis.