Seurat: Tools for Single Cell Genomics

Canonical link: https://rscholar.com/pkg/Seurat

Andrew Butler • Saket Choudhary • David Collins • Charlotte Darby • Jeff Farrell • Isabella Grabski • Christoph Hafemeister • Yuhan Hao • Austin Hartman • Paul Hoffman • Jaison Jain • Longda Jiang • Madeline Kowalski • Skylar Li • Gesmira Molla • Efthymia Papalexi • Patrick Roelli • Rahul Satija • Karthik Shekhar • Avi Srivastava • Tim Stuart • Kristof Torkenczy • Shiwei Zheng • Satija Lab • Collaborators • View description and downloads View dependencies GitHub project

2017 Published

0 Citations

25 Authors

43 Revisions

5.4.0 Version

MIT License

Referenced by ⇅	Year
CSCDRNA: Covariance Based Single-Cell Decomposition of Bulk Expression Data (Version 1.0.3)	2022
DUBStepR: Correlation-Based Feature Selection for Single-Cell RNA Sequencing Data (Version 1.2.0)	2021
maple: Bayesian Analysis of Multi-Sample Spatial Transcriptomics Experiments (Version 0.99.5)	2022
PALMO: Identify Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset (Version 0.1.2)	2022
spruce: Spatial Random Effects Clustering of Single Cell Data (Version 0.99.1)	2022
gsdensity: Density-Based Gene Set Specificity Evaluation (Version 0.1.2)	2023
countland: Analysis of Biological Count Data, Especially from Single-Cell RNA-Seq (Version 0.1.2)	2022
APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles (Version 1.3.0)	2023
BisqueRNA: Decomposition of Bulk Expression with Single-Cell Sequencing (Version 1.0.5)	2019
CACIMAR: Cross-Species Analysis of Cell Identities, Markers and Regulations (Version 1.0.0)	2022
CAESAR.Suite: CAESAR: a Cross-Technology and Cross-Resolution Framework for Spatial Omics Annotation (Version 0.3.0)	2024
CAMML: Cell-Typing using Variance Adjusted Mahalanobis Distances with Multi-Labeling (Version 1.0.0)	2021
CIDER: Meta-Clustering for scRNA-Seq Integration and Evaluation (Version 0.99.4)	2021
CytoSimplex: Simplex Visualization of Cell Fate Similarity in Single-Cell Data (Version 0.2.0)	2023
DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics (Version 1.2.3)	2020
DWLS: Gene Expression Deconvolution Using Dampened Weighted Least Squares (Version 0.1.0)	2022
HetSeq: Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity (Version 0.1.0)	2025
PRECAST: Embedding and Clustering with Alignment for Spatial Omics Datasets (Version 1.8)	2022
PoweREST: A Bootstrap-Based Power Estimation Tool for Spatial Transcriptomics (Version 0.1.2)	2024
ProFAST: Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction (Version 1.7)	2023
SCIntRuler: Guiding the Integration of Multiple Single-Cell RNA-Seq Datasets (Version 0.99.6)	2024
SCORPIUS: Inferring Developmental Chronologies from Single-Cell RNA Sequencing Data (Version 1.0.10)	2017
SCRIP: An Accurate Simulator for Single-Cell RNA Sequencing Data (Version 1.0.0)	2021
SCdeconR: Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq Data as Reference (Version 1.0.0)	2024
SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data (Version 3.0.1)	2022
SPECK: Receptor Abundance Estimation using Reduced Rank Reconstruction and Clustered Thresholding (Version 1.0.1)	2022
STREAK: Receptor Abundance Estimation using Feature Selection and Gene Set Scoring (Version 1.0.0)	2022
SignacX: Cell Type Identification and Discovery from Single Cell Gene Expression Data (Version 2.2.5)	2021
SuperCell: Simplification of scRNA-Seq Data by Merging Together Similar Cells (Version 1.1)	2024
dyngen: A Multi-Modal Simulator for Spearheading Single-Cell Omics Analyses (Version 1.0.5)	2020
easybio: Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit (Version 1.2.3)	2024
nebula: Negative Binomial Mixed Models Using Large-Sample Approximation for Differential Expression Analysis of ScRNA-Seq Data (Version 1.5.6)	2022
rPanglaoDB: Download and Merge Single-Cell RNA-Seq Data from the PanglaoDB Database (Version 0.2.1)	2021
scAnnotate: An Automated Cell Type Annotation Tool for Single-Cell RNA-Sequencing Data (Version 0.3)	2022
scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing (Version 3.2.4)	2022
scGOclust: Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq (Version 0.2.1)	2023
scDiffCom: Differential Analysis of Intercellular Communication from scRNA-Seq Data (Version 1.2.0)	2021
scGate: Marker-Based Cell Type Purification for Single-Cell Sequencing Data (Version 1.7.2)	2022
scPipeline: A Wrapper for 'Seurat' and Related R Packages for End-to-End Single Cell Analysis (Version 0.2.0.0)	2025
scaper: Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation (Version 0.2.0)	2023
scregclust: Reconstructing the Regulatory Programs of Target Genes in scRNA-Seq Data (Version 0.2.2)	2024
CAMML Multi-Labeling: (Version )	0
cellpypes: Cell Type Pipes for Single-Cell RNA Sequencing Data (Version 0.3.0)	2022
ggsector: Draw Sectors (Version 1.7.0)	2022
ClustAssess: Tools for Assessing Clustering (Version 1.1.0)	2021
ClusterGVis: One-Step to Cluster and Visualize Gene Expression Data (Version 0.1.4)	2025
CytoSimplex Data: (Version )	0
APackOfTheClones Profiles: (Version )	0
AnanseSeurat: Construct ANANSE GRN-Analysis Seurat (Version 1.2.0)	2023
CACIMAR Regulations: (Version )	0
CIARA: Cluster Independent Algorithm for Rare Cell Types Identification (Version 0.1.0)	2022
CRMetrics: Cell Ranger Output Filtering and Metrics Visualization (Version 0.3.2)	2022
Canek: Batch Correction of Single Cell Transcriptome Data (Version 0.2.5)	2022
DIscBIO Transcriptomics: (Version )	0
DR.SC: Joint Dimension Reduction and Spatial Clustering (Version 3.7)	2021
DWLS Squares: (Version )	0
DamageDetective: Detecting Damaged Cells in Single-Cell RNA Sequencing Data (Version 1.0.0)	2025
GeneNMF: Non-Negative Matrix Factorization for Single-Cell Omics (Version 0.9.2)	2024
PRECAST Datasets: (Version )	0
Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis (Version 3.6.0)	2021
PopComm: Population-Level Cell-Cell Communication Analysis Tools (Version 1.0.0)	2025
PoweREST Transcriptomics: (Version )	0
ProFAST Reduction: (Version )	0
RESET: Reconstruction Set Test (Version 1.0.0)	2023
RepeatedHighDim: Methods for High-Dimensional Repeated Measures Data (Version 2.5.0)	2011
SeuratExplorer 'Seurat': (Version )	0
Signac: Analysis of Single-Cell Chromatin Data (Version 1.16.0)	2020
SlideCNA: Calls Copy Number Alterations from Slide-Seq Data (Version 0.1.0)	2025
SoupX: Single Cell mRNA Soup eXterminator (Version 1.6.2)	2020
SpaCCI: Spatially Aware Cell-Cell Interaction Analysis (Version 1.0.4)	2024
SuperCell Cells: (Version )	0
VAM: Variance-Adjusted Mahalanobis (Version 1.1.0)	2021
XYomics: Analysis of Sex Differences in Omics Data for Complex Diseases (Version 0.1.3)	2025
bbknnR: Perform Batch Balanced KNN in R (Version 2.0.2)	2022
clustree: Visualise Clusterings at Different Resolutions (Version 0.5.1)	2018
combiroc: Selection and Ranking of Omics Biomarkers Combinations Made Easy (Version 0.3.4)	2021
conos: Clustering on Network of Samples (Version 1.5.2)	2021
countland RNA-Seq: (Version )	0
dyngen Analyses: (Version )	0
easybio Toolkit: (Version )	0
grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data (Version 0.2.7)	2022
harmony: Fast, Sensitive, and Accurate Integration of Single Cell Data (Version 1.2.4)	2021
mLLMCelltype: Cell Type Annotation Using Large Language Models (Version 1.3.2)	2025
mascarade Plots: (Version )	0
mixhvg: Mixture of Multiple Highly Variable Feature Selection Methods (Version 1.0.1)	2022
mxfda: A Functional Data Analysis Package for Spatial Single Cell Data (Version 0.2.2-1)	2024
myTAI: Evolutionary Transcriptomics (Version 2.3.4)	2014
rPanglaoDB Database: (Version )	0
rliger: Linked Inference of Genomic Experimental Relationships (Version 2.2.1)	2021
scGOclust RNA-Seq: (Version )	0
scGate Data: (Version )	0
scMappR: Single Cell Mapper (Version 1.0.12)	2020
scMetaTraj Data: (Version )	0
scRNAstat: A Pipeline to Process Single Cell RNAseq Data (Version 0.1.1.1)	2021
sccca: Single-Cell Correlation Based Cell Type Annotation (Version 0.1.1)	2024
sccore: Core Utilities for Single-Cell RNA-Seq (Version 1.0.6)	2020
scperturbR: E-Statistics for Seurat Objects (Version 0.1.0)	2023
scpoisson: Single Cell Poisson Probability Paradigm (Version 0.0.2)	2022
tidyseurat: Brings Seurat to the Tidyverse (Version 0.8.7)	2020
treefit: The First Software for Quantitative Trajectory Inference (Version 1.0.3)	2020

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