Overview
As a database dedicated to single-cell plants, our goal is to offer a wide range of valuable tools and a wealth of data for our users to utilize. We are pleased to provide a comprehensive user guide for our database, and we hope that you will find it both informative and enjoyable to use.
What does scPlantDB have?
scPlantDB mainly provides four modules:
Browser - Including meta information, CellxGene compatibility, comparative analysis, and download options for both .rds and .h5ad file formats for our dataset.
Marker - Including summary and detailed marker tables, as well as GSEA and Ortho gene analysis, for each cell type across different species.
Tools - Including three essential tools: Blast, Cell Type Comparator, and Cell Type Predictor.
Search - Two seacrch methods, include keyword search (marker and cell type) and sequence search using Blast.
Main features of scPlantDB
Comprehensive and Harmonized Data
scPlantDB serves as a comprehensive and plant-specific database, offering the largest collection of plant single-cell transcriptome datasets. Currently, it comprises 2002109 cells from 54 datasets/304 experiments across 13 plant species and will be regularly updated with new datasets as they become available.
Interactive visualization
The Dataset Module presents all meta-information and enables easy visualization of multiple-dataset comparisons via feature plots, violin plots, and heatmaps. Additionally, the single-dataset exploration feature utilizes cellxgene (Megill et al., 2021) to facilitate data exploration.
Analysis tools
scPlantDB includes the Marker Module, which enables the analysis of the expression and function of cell-type-specific markers from different experiments within the same plant species. It also enables the exploration of cellular comparisons across different plant species. Additionally, the platform offers two online tools for Cell type comparator and predictor, both of which are marker-based.