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scPlant

scPlant: a versatile framework for single-cell transcriptomic data analysis in plants.

The scPlant pipeline is implemented with plentiful functions for diverse analytical tasks, ranging from basic data processing to advanced demands such as cell type annotation and deconvolution, trajectory inference, cross-species data integration and cell-type specific gene regulatory network construction.

Installation

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

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

Then, install scPlant:

devtools::install_github("compbioNJU/scPlant")

Usage

Please see website: https://compbioNJU.github.io/scPlant

Citation:

Cao, S., He, Z., Chen, R., Luo, Y., Fu, L.-Y., Zhou, X., He, C., Yan, W., Zhang, C.-Y., Chen, D., scPlant: a versatile framework for single-cell transcriptomic data analysis in plants, PLANT COMMUNICATIONS (2023), doi: https://doi.org/10.1016/j.xplc.2023.100631.

Please note that MINI-EX uses a dual license to offer the distribution of the software under a proprietary model as well as an open source model.