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_pkgdown.yaml
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url: https://satijalab.org/seurat
destination: docs
template:
params:
bootswatch: flatly
ganalytics: UA-82807227-1
docsearch:
api_key: ead918d7fe8467a2fd38e97f5bbe3ecb
index_name: seurat
navbar:
title: "Seurat"
left:
- text: "Install"
href: articles/install_v5.html
- text: "Get started"
href: articles/get_started_v5_new.html
- text: "Vignettes"
menu:
- text: Introductory Vignettes
- text: "PBMC 3K guided tutorial"
href: articles/pbmc3k_tutorial.html
- text: "Data visualization vignette"
href: articles/visualization_vignette.html
- text: "SCTransform, v2 regularization"
href: articles/sctransform_vignette.html
- text: "Using Seurat with multi-modal data"
href: articles/multimodal_vignette.html
- text: "Seurat v5 Command Cheat Sheet"
href: articles/essential_commands.html
- text: -------
- text: Data Integration
- text: "Introduction to scRNA-seq integration"
href: articles/integration_introduction.html
- text: "Integrative analysis in Seurat v5"
href: articles/seurat5_integration.html
- text: "Mapping and annotating query datasets"
href: articles/integration_mapping.html
- text: -------
- text: Multi-assay data
- text: "Dictionary Learning for cross-modality integration"
href: articles/seurat5_integration_bridge.html
- text: "Weighted Nearest Neighbor Analysis"
href: articles/weighted_nearest_neighbor_analysis.html
- text: "Integrating scRNA-seq and scATAC-seq data"
href: articles/seurat5_atacseq_integration_vignette.html
- text: "Multimodal reference mapping"
href: articles/multimodal_reference_mapping.html
- text: "Mixscape Vignette"
href: articles/mixscape_vignette.html
- text: -------
- text: Massively scalable analysis
- text: "Sketch-based analysis in Seurat v5"
href: articles/seurat5_sketch_analysis.html
- text: "Sketch integration using a 1 million cell dataset from Parse Biosciences"
href: articles/ParseBio_sketch_integration.html
- text: "Map COVID PBMC datasets to a healthy reference"
href: articles/COVID_SCTMapping.html
- text: "BPCells Interaction"
href: articles/seurat5_bpcells_interaction_vignette.html
- text: -------
- text: Spatial analysis
- text: "Analysis of spatial datasets (Imaging-based)"
href: articles/seurat5_spatial_vignette_2.html
- text: "Analysis of spatial datasets (Sequencing-based)"
href: articles/spatial_vignette.html
- text: -------
- text: Other
- text: "Cell-cycle scoring and regression"
href: articles/cell_cycle_vignette.html
- text: "Differential expression testing"
href: articles/de_vignette.html
- text: "Demultiplexing with hashtag oligos (HTOs)"
href: articles/hashing_vignette.html
- text: Extensions
href: articles/extensions.html
- text: FAQ
href: "https://github.com/satijalab/seurat/discussions"
- text: "News"
href: articles/announcements.html
- text: "Reference"
href: reference/index.html
- text: "Archive"
href: articles/archive.html
right:
- icon: fa-home
href: ../
- icon: fa-github
href: https://github.com/satijalab/seurat
reference:
- title: "Object interaction"
desc: "Functions for interacting with a Seurat object"
- contents:
- has_concept("objects")
- title: "Preprocessing"
desc: "Functions for preprocessing single-cell data"
- contents:
- has_concept("preprocessing")
- title: "Differential expression"
desc: "Functions for testing differential gene (feature) expression"
- contents:
- has_concept("differential_expression")
- title: "Dimensional Reduction"
desc: "Functions to reduce the dimensionality of datasets"
- contents:
- has_concept("dimensional_reduction")
- title: "Clustering"
desc: "Functions to cluster single-cell data"
- contents:
- has_concept("clustering")
- title: "Integration"
desc: >
Functions related to the Seurat v3 integration and label transfer algorithms
- contents:
- has_concept("integration")
- title: "Spatial"
desc: >
Functions related to the analysis of spatially-resolved single-cell data
- contents:
- has_concept("spatial")
- title: "Sketching"
desc: "Functions for flexible analysis of massively scalable datasets"
- contents:
- has_concept("sketching")
- title: "Mixscape"
desc: >
Functions related to the mixscape algorithm
- contents:
- has_concept("mixscape")
- title: "Visualization"
desc: "Functions for plotting data and adjusting"
- contents:
- has_concept("visualization")
- title: "Tree-related functions"
desc: "Function related to tree-based analysis of identity classes"
- contents:
- has_concept("tree")
- title: "Utility functions"
desc: "Useful functions to help with a variety of tasks"
- contents:
- has_concept("utilities")
- title: "Data"
desc: "Descriptions of data included with Seurat"
- contents:
- has_concept("data")
- title: "Convenience functions"
desc: "Functions included for user convenience and to keep maintain backwards compatability"
- contents:
- has_concept("convenience")
- title: "Sketching"
desc: "Functions for flexible analysis of massively scalable datasets"
- contents:
- has_concept("sketching")
- title: "Re-exports"
desc: "Functions re-exported from other packages"
- contents:
- reexports
- Seurat-class
- Assay-class
- DimReduc-class
- Neighbor-class
- Graph-class
- SpatialImage-class
- JackStrawData-class
- SeuratCommand-class
- Seurat-package