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).
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.
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
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
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
Arabidopsis across development, Lee et al. dataset, nuclei across all Arabidopsis tissues and developmental stages
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)
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
NCBI Gene Expression Omnibus
Genome Sequence Archive
China National Center for Bioinformaiton (CNCB) genome sequence archive
China National Center for Bioinformaiton (CNCB) genome sequence archive
PlantCellMarker
Single-cell markers
Single-cell markers
Processing and annotation tools
Cytoscape
Software platform for visualizing complex networks and integrating these with any type of attribute data
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
R package implementing method described in Quantification of cell identity from single-cell gene expression profiles
STAR
STAR tools for preprocessing RNA-seq data (including STARsolo for scRNA-seq)
Dobin et al. 2013 doi.org/10.1093/bioinformatics/bts635
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
Single-Cell Aggregation for High Resolution Cell States
Seurat v5
General single-cell processing tool
General single-cell processing tool
diem
Software for estimating ambient RNA for single nuclei/cells
Software for estimating ambient RNA for single nuclei/cells
Socrates
scATAC-seq data analysis tool (Bob Schmitz Lab)
scATAC-seq data analysis tool (Bob Schmitz Lab)
Docker
Version control for analysis environments
Version control for analysis environments
COPO
Brokering tool for submitting sample, read, assembly, annotation, and (soon) single cell rna-SEQ
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
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
Tutorial/Presentations/Troubleshooting
Stack Overflow
General-purpose troubleshooting site - if you run into a bug using most software, chances are someone else has posted a fix here.
General-purpose troubleshooting site - if you run into a bug using most software, chances are someone else has posted a fix here.
