Analyses of high-throughput data from heterogeneous samples with TOAST
Introduction | Installation and quick start | Install TOAST | How to get help for TOAST | Quick start on detecting cell type-specific differential signals | Example dataset | Estimate mixing proportions | Reference-based deconvolution using least square method | Reference-free deconvolution using RefFreeEWAS | Improve reference-free deconvolution with cross-cell type differential analysis | Improved-RF with myRefFreeCellMix | Improved-RF with use-defined RF function | Partial reference-free deconvolution (TOAST/-P and TOAST/+P) | Choose cell type-specific markers | PRF deconvolution without prior (TOAST/-P) | PRF deconvolution with prior (TOAST/+P) | Complete deconvolution using a geometric approach | Detect cell type-specific and cross-cell type differential signals | Detect cell type-specific differential signals under two-group comparison | Testing one parameter (e.g. disease) in one cell type. | Testing one parameter in all cell types. | Testing one parameter in all cell types by incorporating DE/DM state correlation among cell types | Detect cell type-specific differential signals from a general experimental design | Testing one parameter in one cell type | Testing the joint effect of single parameter in all cell types. | Detect cross-cell type differential signals | Testing cross-cell type differential signals in cases (or in controls). | Testing the overall cross-cell type differences in all samples. | Testing the differences of two cell types over different values of one phenotype (higher-order test). | A few words about variance bound and Type I error. | Variance bound | Type I error | Session info
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