Due to an updated version of SCTransform (‘v2’) function, we should run PrepSCTFindMarkers() before running FindMarkers(). So, we updated the corresponding R code (using_example.ipynb). 2022-08-22
add marker genes for Fragaria vesca, Populus, Nicotiana attenuata and Lemna minuta. 2022-08-21
The woodland strawberry (Fragaria vesca) leaves single-cell RNA-seq dataset are processing. 2022-08-17
Our article "PlantPhoneDB: A manually curated pan‐plant database of ligand‐receptor pairs infers cell–cell communication" was Published Online. To access the article, please click the following link: https://onlinelibrary.wiley.com/doi/10.1111/pbi.13893
PlantPhoneDB R package successfully passed security detection by OSCS.
We provided a new link for some updates about website. The link is https://jasonxu.shinyapps.io/website/. 2022-08-08
Chaoqun Xu#, Dongna Ma#, Qiansu Ding, Ying Zhou*, Hai-Lei Zheng*. PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. (Plant Biotechnology Journal; Impact Factor 13.263; accepted )
PlantSCI: A Single Cell shiny application for Identification of cell-cell communication. coming soon: 2022-03-20
Developing a Rshiny app for analyzing and visualizing in single cell RNA-seq data. 2022-02-25
A full documentation for PlantPhoneDB is available at https://plantphonedb.readthedocs.io/en/latest/index.html. 2022-02-15
Add help document for functions, such as LRscore, LR_pathway, etc. 2022-02-13 (Version 1.0.0)
The PlantPhoneDB-Tutorial coming soon: 2022-01-23
Last package update: 2021-10-26
Welcome! This is the documentation for PlantPhoneDB (see in detail), a manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. The web server address is https://jasonxu.shinyapps.io/PlantPhoneDB/
To install it, the easiest way is to use the R package devtools and its function install_github. If you don't have all the dependancies needed to use PlantPhoneDB package, run the commands below:
install.packages(c("devtools", "Seurat", "tidyverse", "ggplot2", "ggsci", "pheatmap", "ggpubr", "RColorBrewer", "patchwork", "lsa", "viridis", "hrbrthemes", "circlize", "chorddiag", "ggplotify", "data.table", "parmigene", "infotheo", "igraph", "cowplot", "grid", "dplyr")) ##Installs devtools and the PlantPhoneDB CRAN dependancies
Then you just have to load devtools package and run the command below:
library(devtools)
install_github("Jasonxu0109/PlantPhoneDB")
Once all the dependencies are downloaded and loaded, you can load the ‘PlantPhoneDB’ package.
Examples on how to use PlantPhoneDB package functions can be found as below:
Case1.ipynb was used to infer cell-cell communications from scRNA-seq datasets processed by using_example.ipynb .
Case 2. Compare the number of interactions among cell types between two datasets (93-11 and Nipponbare)
Please cite the following paper if you used PlantPhoneDB in your research.
Xu, C., Ma, D., Ding, Q., Zhou, Y., and Zheng, H.-L. (2022) PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. Plant Biotechnology Journal, 2022, 20, doi: 10.1111/pbi.13893.