This protocol page contains reproducible workflows for different types of analysis using Spectre. For those gettings started with analysis, you can also check out these two commentary papers where we provide considerations for new and experienced users in the design and analysis of high-dimensional experiments: Marsh-Wakefield et al 2021 (ICB), Liechti et al 2021 (Nature Immunology). For more educational content you can check out the tutorials page.
Data preparation
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Initial data preparation Here we provide instructions for initial data preparation, including compensation, cleanup gating, and data export from programs such as FlowJo. For cell isolation and staining protocols for flow, spectral, or mass (CyTOF) cytometry, please see our resources page. GO TO PAGE
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Core analysis workflows
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Simple discovery workflow
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Discovery workflow with batch alignment using CytoNorm
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| A simple workflow (with worked example) using a single R script (or single FlowJo workspace) to run clustering/dimensionality reduction, make plots, and perform some limited quantitative/statistical analysis. No batch alignment steps included. | A analysis workflow for the alignment and analysis of data from multiple batches, using CytoNorm for batch alignment. If working with very large batch effects, have a look at our data integration workflows. |
Quick analysis scripts
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Rapidly generate tSNE or UMAP plots from CSV or FCS files
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Convert CSV to FCS files (and vise versa)
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Rapid generation of graphs and heatmaps for quantitative, differential, and statistical analysis
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| An R script to automatically generate tSNE or UMAP plots, after tSNE or UMAP has run in programs such as FlowJo. | An R script to rapidly convert FCS files to CSV files (or vise versa). | Here we present a quick workflow script to rapidly generate graphs and heatmaps for quantitative, differential, and statistical analysis. Note, this can be used on summary data generated by any program, including FlowJo. |
Specialised analysis areas
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Time-series analysis
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scRNAseq analysis
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Automated cell classification
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| Here we provide a time-series clustering workflow using TrackSOM. | Here we provide analysis options and tools to support scRNAseq analysis, in conjunction with existing tools such as Seurat and SingleCellExperiment. | Strategies to facilitate automated cell classification. |