LRLoop

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.

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Quick Installation of LRLoop

First, install devtools (for installing GitHub packages) if it isn't already installed

if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")

Then, install nichenetr if it isn't already installed

devtools::install_github("saeyslab/nichenetr")

Then, install all of the LRLoop dependencies

install.packages(c('tidyverse','Seurat','ggplot2','dplyr','circlize','igraph','RColorBrewer','writexl','pheatmap'))

Lastly, install LRLoop

devtools::install_github('https://github.com/Pinlyu3/LRLoop',force = TRUE)

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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

• Perform LRLoop analysis starting from Seurat objects

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Issues using LRLoop?

LRLoop is currently in beta. If you think you have found a bug, please report an issue on Github with the Bug Report form.