Issues on Mac OS X1 months ago
Install TBB using brew | Install RcppParallel with TBB path | Session info
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Using crumblr in practice3 months ago
Introduction | Installation | Analysis workflow | Process data | Variance partitioning | PCA | Hierarchical clustering | Differential testing | Multivariate testing along a tree | Combined plotting | Considerations | Computational scaling | Complex study designs | Tuning parameters | Session Info
Normal approximation vs. empirical simulation3 months ago
Simulations | D=2 categories | D=15 categories | Session Info
Integration with dreamlet / SingleCellExperiment3 months ago
Load and process single cell data | Aggregate to pseudobulk | Process data | Analysis | Multivariate testing along a tree | Session Info
Extending GenomicDataStream12 months ago
Additional file types | Additional matrix types | Importing into other projects
Reading data as a GenomicDataStream12 months ago
Usage | Example code with R | Read genotype data into R | Use R to run analysis at C++ level | Example code with C++17 | Data types | Session info
Fast Whitening Transformation1 years ago
Basic usage | Advanced usage | Directly compute whitening matrix | Explicit covariance or correlation | Sample from multivariate normal | Low-rank models | Computing condition number | Removing correlation vs covariance | Session Info
Loading gene sets2 years ago
Easy loading of gene set databases | Other databases | Custom gene sets | Session Info
Modeling continuous cell-level covariates2 years ago
Introduction | Standard processing | Pseudobulk | Analysis | Details | Session Info
Handling large H5AD datasets2 years ago
Introduction | On-disk storage: zellkonverter | Standard usage | Merge multiple datasets | Access alternative data | In-memory storage: Seurat | Comparing interfaces | Session Info
Dreamlet analysis of single cell RNA-seq2 years ago
Introduction | Installation | Process single cell count data | Preprocess data | Aggregate to pseudobulk | Voom for pseudobulk | Variance partitioning | Differential expression | Volcano plots | Gene-level heatmap | Extract results | Forest plot | Box plot | Advanced used of contrasts | Gene set analysis | Heatmap of top genesets | All gene sets with FDR < 30% | Comparing expression in clusters | Gene-cluster specificity | Session Info
Error handling3 years ago
Errors with random effects | Errors at the assay- and gene-level | Assay-level errors | Gene-level errors | Session Info
Testing non-linear effects3 years ago
Introduction | Standard processing | Continuous variable | Ordered categorical | Sample filtering | Session Info
mashr analysis after dreamlet3 years ago
Instroduction | Standard dreamlet analysis | Preprocess data | Aggregate to pseudobulk | dreamlet for pseudobulk | Run mashr analysis | Summarize mashr results | Gene set analysis | Session Info
Random effects meta-analysis for correlated test statistics3 years ago
Fixed effects meta-analysis | Random effects meta-analysis | Examples | Session info | References
Zenith gene set testing after dream analysis4 years ago
Standard workflow | Session Info