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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Seurat Resource Report Resource Website 10000+ mentions |
Seurat (RRID:SCR_016341) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data. | single, cell, genomic, RNA-seq, data, QC, analysis, source, heterogeneity, transcriptomic, measurement, integrate, diverse |
is used by: Stardust is used by: Seurat MapQuery is used by: scSidekick is related to: DoubletFinder is related to: Azimuth works with: SeuratWrappers works with: Connectome |
NHGRI 1DP2HG009623; NIMH 5R01MH071679; NSF |
PMID:29608179 | Free, Available for download, Freely available | https://satijalab.org/seurat/get_started.html | SCR_016341 | 2026-08-29 11:28:07 | 11480 | |||||||
|
Azimuth Resource Report Resource Website 50+ mentions |
Azimuth (RRID:SCR_021084) | software resource, web application | Web application that uses annotated reference dataset to automate processing, analysis, and interpretation of new single cell RNA-seq experiment. Azimuth leverages reference based mapping, pipeline that inputs counts matrix of gene expression in single cells, and performs normalization, visualization, cell annotation, and differential expression. All results can be explored within the app, and easily downloaded for additional downstream analysis. | HubMap, BICCN, biomarker discovery, molecular reference maps, annotated reference dataset, automate processing, automate analysis, new single cell RNA-seq experiment interpretation |
is used by: BICCN is used by: The Human BioMolecular Atlas Program is related to: Seurat is related to: Allen Institute for Brain Science |
DOI:10.1101/2020.10.12.335331 | Free, Freely available | SCR_021084 | 2026-08-29 11:27:55 | 75 | |||||||||
|
SeuratWrappers Resource Report Resource Website 10+ mentions |
SeuratWrappers (RRID:SCR_022555) | software resource, software toolkit | Software R package that helps format Seurat objects into objects that can be used for trajectory analysis in other packages such as Monocle | helps format Seurat objects, trajectory analysis, Monocle |
is related to: Seurat MapQuery works with: Seurat |
Free, Available for download, Freely available | SCR_022555 | 2026-08-29 11:31:30 | 40 | ||||||||||
|
Stardust Resource Report Resource Website 1+ mentions |
Stardust (RRID:SCR_022514) | software resource, software toolkit | Software tool for integration of spatial information in spatial transcriptomics data clustering. | Integration of spatial information, spatial transcriptomics data clustering, data clustering |
uses: Seurat uses: rCASC |
Free, Available for download, Freely available | SCR_022514 | 2026-08-29 11:31:32 | 4 | ||||||||||
|
DoubletFinder Resource Report Resource Website 1000+ mentions |
DoubletFinder (RRID:SCR_018771) | data analysis software, data processing software, software application, software resource | Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data. | Doublet detection in single cell RNA, single cell RNA, doublet detection, RNA sequencing data, gene expression data, artificial nearest neighbors |
is related to: Seurat has parent organization: University of California at San Francisco; California; USA |
Damon Runyon Cancer Research Foundation ; Department of Defense Breast Cancer Research Program ; NICHD DP2 HD080351; NSF Science and Technology Center ; NSF MCB 1330864; UCSF Center for Cellular Construction |
PMID:30954475 | Free, Available for download, Freely available | SCR_018771 | 2026-08-29 11:26:13 | 1250 | ||||||||
|
Connectome Resource Report Resource Website 1+ mentions |
Connectome (RRID:SCR_028632) | software resource, software toolkit, source code | Software R package for calculation and interactive exploration of cell-cell signaling network topologies contained in single-cell RNA-sequencing data. Used to explore cell-cell connectivity patterns based on ligand and receptor data in heterogeneous single-cell datasets. | calculation and interactive exploration of cell-cell signaling network, network topologies, single-cell RNA-sequencing data, explore cell-cell connectivity patterns, ligand and receptor data, heterogeneous single-cell datasets, | works with: Seurat | DOI:10.1101/2021.01.21.427529 | Free, Available for download, Freely available | SCR_028632 | 2026-08-29 11:35:50 | 2 | |||||||||
|
Seurat MapQuery Resource Report Resource Website |
Seurat MapQuery (RRID:SCR_027590) | software application, software resource | Convenience wrapper function around the following three functions that are often run together when mapping query data to a reference: TransferData, IntegrateEmbeddings, ProjectUMAP. | Convenience wrapper function, mapping query data to reference, |
uses: Seurat is related to: SeuratWrappers |
Free, Freely available | SCR_027590 | 2026-08-29 11:35:30 | 0 | ||||||||||
|
scSidekick Resource Report Resource Website |
scSidekick (RRID:SCR_028835) | software resource, software toolkit, source code | Software single-cell RNA-seq and spatial transcriptomics R toolkit built on top of Seurat. It wraps repetitive boilerplate into one-liners, enforces consistent colors and layouts across an entire project, and automates the last mile from analysis to slide deck. | single-cell RNA-seq, spatial transcriptomics, wraps repetitive boilerplate into one-liners, enforces consistent colors and layoutst, automates last mile from analysis to slide deck, | uses: Seurat | Free, Available for download, Freely available | https://zenodo.org/records/21285418 | SCR_028835 | 2026-08-29 11:35:50 | 0 |
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