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Spectre tutorials

The protocol pages contain specific and reproducible workflows for different types of analysis using Spectre. The tutorials provided on this page are intended to educate users on various aspects of analysis, or to showcase unique or bespoke uses of Spectre, which may go on to become stable workflows if there is sufficient interest from users. If there is content on this page you would like to see more of, or you would like to see turned into a standard workflow, then please drop us a note on our Q&A page or email us.

Project planning

Planning your high-dimensional experiments
High-dimensional data analysis
An open access publication where we provide considerations for new and experienced users to design and carry out high‐dimensional experiments to maximize quality data collection. A paper discussing common caveats and best practices in the analysis of high-dimensional cytometry data

Analysis strategies

Introduction to computational analysis approaches
How many cells can I analyse?
Which markers should I use for clustering?

A brief introduction to the advantages and disadvantages of computational 'discovery' approaches, including clustering and dimensionality reduction. A brief tutorial on assessing how many cells can be analysed using popular clustering (e.g. FlowSOM) and dimensionality reduction (e.g. tSNE, UMAP) techniques. A brief tutorial on determining which markers to use for clustering and dimensionality reduction.

General data manipulation and plotting

Arcsinh transformation
Manipulating and filtering data with data.table
Make great plots with Spectre ggplot2
A tutorial on transformations for cytometry data, specifically using the arcsinh transformations. A tutorial on rapid data manipulation and filtering operations for large datasets using data.table. Instructions for creating high-quality coloured tSNE/UMAP plots using Spectre's wrapper for ggplot2.

Quantitative, differential, and statistical analysis including heatmaps

Generating 'summary' data
Creating heatmaps
Creating comparison graphs/violing plots
A tutorial on generating 'summary' data from analysed 'cellular' data, to be used for quantitative, differential, and statistical analysis. A tutorial on the use of expression and z-score/fold-change heatmaps in Spectre. A tutorial on the generation of comparison graphs/violin plots in Spectre.

Code for the table structure adapted from https://satijalab.org/seurat

Batch alignment and data integration

Tutorial on batch alignment approaches for minor batch effects.
Tutorial on strategies to integrate data across batches, experiments, panels, and technologies.
A brief tutorial on batch alignment approaches for cytometry data. A brief tutorial on data integration approaches.