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https://github.com/Pinlyu3/LRLoop
LRLoop
https://github.com/Pinlyu3/LRLoop
Last synced: 4 months ago
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LRLoop
- Host: GitHub
- URL: https://github.com/Pinlyu3/LRLoop
- Owner: Pinlyu3
- License: mit
- Created: 2021-06-28T13:58:10.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2022-01-04T23:59:56.000Z (over 2 years ago)
- Last Synced: 2023-07-17T16:17:43.258Z (11 months ago)
- Language: R
- Homepage:
- Size: 256 MB
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Lists
- awesome-cell-cell-communication - LRLoop - [R]- LRLoop is a full-featured R package for analyzing LR-Loops from bulk & single-cell RNA-seq data. (Uncategorized / Uncategorized)
README
# LRLoop
[](https://www.tidyverse.org/lifecycle/#maturing) [](https://github.com/Pinlyu3/LRLoop/actions/workflows/R-CMD-check.yaml)
LRLoop is a full-featured R package for analyzing LR-Loops from bulk & single-cell RNA-seq data.
### LRLoop is currently in beta and will be in active development through the peer review process.
## Quick Installation of LRLoop
**First, install devtools (for installing GitHub packages) if it isn't already installed**
```{r}
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
```
**Then, install nichenetr if it isn't already installed**
```{r}
devtools::install_github("saeyslab/nichenetr")
```
**Then, install all of the LRLoop dependencies**
```{r}
install.packages(c('tidyverse','Seurat','ggplot2','dplyr','circlize','igraph','RColorBrewer','writexl','pheatmap'))
```
**Lastly, install LRLoop**
```{r}
devtools::install_github('https://github.com/Pinlyu3/LRLoop',force = TRUE)
```
## Learning to use LRLoop
To learn how to use LRLoop, read the following vignettes explaining several types of analyses:
- The datasets in vignettes can be downloaded from [google drive](https://drive.google.com/drive/folders/1WV0iSlAXCUwSZMSBnzsHdZc26RuyfunC?usp=sharing)
- [Perform LRLoop analysis starting from Seurat objects](vignettes/Main.md)
## Issues using LRLoop?
LRLoop is currently in __beta__. If you think you have found a bug, please [report an issue on Github](https://github.com/Pinlyu3/LRLoop/issues) with the __Bug Report__ form.