https://github.com/Pinlyu3/LRLoop

LRLoop
https://github.com/Pinlyu3/LRLoop

Last synced: 3 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 (over 3 years ago)
• Default Branch: main
• Last Pushed: 2022-01-04T23:59:56.000Z (about 3 years ago)
• Last Synced: 2024-08-03T14:06:59.789Z (6 months ago)
• Language: R
• Homepage:
• Size: 256 MB
• Stars: 3
• Watchers: 1
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

Awesome Lists containing this project

• 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

 [![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) [![example event parameter](https://github.com/Pinlyu3/LRLoop/actions/workflows/R-CMD-check.yaml/badge.svg)](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.