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Giotto
4.2.0
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Giotto Installation
Giotto Ecosystem
Giotto Class Structure
General Giotto Workflow
Giotto Core Functions
FAQs
How to report a bug
Documentation
Examples
Seq-Scope
Mouse liver
Visium
Visium Mouse Kidney
Visium Mouse Brain
Visium Prostate Integration
CytAssist Human Lung Cancer
CytAssist Multi-omics Human Glioblastoma
VisiumHD Human Colorectal Cancer
Slide-seq
Slide-seq Mouse brain
Spatial Genomics
Mouse Kidney
DBiT-Seq
Multi-omics Mouse Embryo DBiT-Seq
Spatial CITE-Seq
Multi-omics Spatial CITE-Seq Human skin
Xenium
Xenium Human breast cancer
Nanostring CosMx
Nanostring CosMx Subcellular Lung Cancer
MERFISH
MERFISH Mouse Hypothalamic Preoptic Region
Vizgen
Vizgen Mouse Brain Receptor Map
Open-ST
Open-ST Mouse Hippocampus
seqFISH
mini seqFISH
SeqFish+ Mouse Cortex Example
osmFISH
osmFISH Mouse SS Cortex
Resolve Bioscience
Resolve Bioscience Breast Cancer Subcellular
Resolve Bioscience Human lung
CODEX
Codex Mouse Spleen
Single Cell RNA Sequencing
Prostate
Prostate Integration
Human Lung Adenocarcinoma
Tutorials
Giotto Object
Object creation
Create a simulated dataset object
Create and change Giotto instructions
Technology-specific importers
Giotto Configuration
Giotto Configuration
Pre-Processing
Feature Aggregation
Analysis
Process Giotto convenience function
Detection of Highly Variable Features
Dimension reduction
Spatial and feature networks
Finding Differential Expressed Genes
Deconvolution
PAGE and Rank Enrichment
Kriging
Tesselation
Spatial Patterns
Detection of spatial genes
Detection of spatial co-expression modules
Spatially Informed clusters
Spatial domain analysis using HMRF
Multiple samples
Multi-sample with integration
Object splitting and joining
Batch effect removal with Harmony
Tissue Microarrays
Spatial manipulation
Spatial transformations
Spatial geometries
Image alignment
Image alignment
Interactivity
Interactive selection
Interactive visualization with vitessceR
Interactive region selection on large datasets
Visualizations
Visualizations
Metafeatures
Cross section
Saving and Loading
Saving a Giotto object
Saving plots
Interoperability
AnnData
Integrate Bento Analysis
Integrate ONTraC Analysis
SpatialExperiment
Seurat
SpatialData
Try Giotto in the Cloud
Giotto on Terra.bio
NeMO Slide-seq on Terra.bio
Containers
Docker
Singularity
Scalability
Using dbMatrix with Giotto
News
Changes
Presentations
Branches
Contributing
Creating a Pull Request
Coding style
Giotto-specific Dispatch Functions
Package imports
Getters and Setters
Python code
Contributing tutorials to the website
Presentations
Source:
vignettes/presentations.Rmd
presentations.Rmd
Giotto workshop 2024
BioC 2023
The Visualization and User Experience Seminars, November 21st 2023
Contents
