Tools and Repositories

Tools, Repositories, and Other Resources

Visualization of scRNA-seq data from Plants

rootcellatlas.org
Integrates preprocessed data from seven Arabidopsis Root studies: (Ryu et al., 2019), (Wendrich et al., 2020), (Zhang et al., 2019), (Denyer et al., 2019), (Jean-Baptiste et al. 2019), (Shulse et al., 2019), (Shahan et al., 2022).

scRNA-Seq Viewer at JGI

scPlantDB
Single Cell Plant DataBase contains re-processed data from many published studies for many species and many tissues. More info can be found in the publication here.

This is a tool and a repository.

Legume Information System
Legume single cell data (currently Medicago root; rhizobia and mock)

Cervantes-Perez et al., 2022 https://doi.org/10.1016/j.molp.2022.10.021

The Plant scRNA-Seq Browser
Includes the Arabidopsis root scRNA-Seq Atlas, the Arabidopsis leaf scRNA-Seq Atlas, and the Wolffia australiana scRNA-Seq Atlas.

Ma et al., 2020 https://doi.org/10.1104/pp.20.00250

ggPlantMap R package
Pre-loaded maps for Arabidopsis (many tissues). Overlay gene expression (or other quantitative data) onto simple images of plant physiology.
Jo and Kajala, 2024 doi.org/10.1093/jxb/erae043

Arabidopsis Developmental Atlas Viewer
Arabidopsis across development, Lee et al. dataset, nuclei across all Arabidopsis tissues and developmental stages

BAR ePlant visualization browser
For Arabidopsis thaliana

Loome
Single-cell visualizations browser from the Lewsey Lab (Latrobe University)

Repositories

Single Cell Expression Atlas

SCEA repository and visualization browser for selected datasets housed at the EBI
13 experiments from Arabidopsis, 3 from rice, 2 from tomato and 2 from maize)

Gene Expression Omnibus

NCBI Gene Expression Omnibus

Sequence Read Archive

NCBI Sequence Read Archive data tool

Genome Sequence Archive

China National Center for Bioinformaiton (CNCB) genome sequence archive

PlantCellMarker

Single-cell markers

Processing and annotation tools

Cytoscape

Software platform for visualizing complex networks and integrating these with any type of attribute data

Index of Cell Identity
R package implementing method described in Quantification of cell identity from single-cell gene expression profiles

CellBender

Software package for eliminating technical artifacts from scRNA-seq data

STAR
STAR tools for preprocessing RNA-seq data (including STARsolo for scRNA-seq)

Dobin et al. 2013 doi.org/10.1093/bioinformatics/bts635

SEACells
Single-Cell Aggregation for High Resolution Cell States

SnapATAC2
scATACseq preprocessing/analysis tool

Signac

scATACseq preprocessing/analysis tool

ArchR

scATACseq preprocessing/analysis tool

Seurat v5

General single-cell processing tool

diem

Software for estimating ambient RNA for single nuclei/cells

Socrates

scATAC-seq data analysis tool (Bob Schmitz Lab)

Docker

Version control for analysis environments

Scanpy

Single-Cell Analysis in Python

Asc-Seurat

Metapackage for single-cell analysis developed on plant datasets

velocyto

Calculate spliced vs unspliced read counts and RNA velocity

dynverse

Metapackage for calculating pseudotime using many different methods

COPO

Brokering tool for submitting sample, read, assembly, annotation, and (soon) single cell rna-SEQ

MINI-EX

MINI-EX is a tool to perform Motif-Informed Network Inference based on single-cell EXpression data and support different plant species.

Staut et al. 2023 bioRxiv: https://doi.org/10.1101/2023.12.24.573246

Infrastructure