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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/satijalab/seurat
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.
Proper citation: Seurat (RRID:SCR_016341) Copy
https://azimuth.hubmapconsortium.org/
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.
Proper citation: Azimuth (RRID:SCR_021084) Copy
https://github.com/satijalab/seurat-wrappers
Software R package that helps format Seurat objects into objects that can be used for trajectory analysis in other packages such as Monocle
Proper citation: SeuratWrappers (RRID:SCR_022555) Copy
https://github.com/InfOmics/stardust
Software tool for integration of spatial information in spatial transcriptomics data clustering.
Proper citation: Stardust (RRID:SCR_022514) Copy
https://github.com/chris-mcginnis-ucsf/DoubletFinder
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.
Proper citation: DoubletFinder (RRID:SCR_018771) Copy
https://github.com/msraredon/Connectome
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.
Proper citation: Connectome (RRID:SCR_028632) Copy
https://satijalab.org/seurat/reference/mapquery
Convenience wrapper function around the following three functions that are often run together when mapping query data to a reference: TransferData, IntegrateEmbeddings, ProjectUMAP.
Proper citation: Seurat MapQuery (RRID:SCR_027590) Copy
https://github.com/nourabdelfattah/scSidekick
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.
Proper citation: scSidekick (RRID:SCR_028835) Copy
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