DecontX has moved to the decontX package11 days ago
DecontX now lives in the decontX package | Installation | Tutorial | Session Information
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Decontamination of ambient RNA in single-cell genomic data with DecontX25 days ago
Introduction | Installation | Importing data | Load PBMC4k data from 10X | Running decontX | Plotting DecontX results | Cluster labels on UMAP | Contamination on UMAP | Expression of markers on UMAP | Barplot of markers detected in cell clusters | Violin plot to compare the distributions of original and decontaminated counts | Other important notes | Choosing appropriate cell clusters | Adjusting the priors to influence contamination estimates | Working with Seurat | Session Information
Analysis of single-cell genomic data with celda25 days ago
Introduction | Installation | Generation of a simulated single cell dataset | Feature selection | Performing bi-clustering with celda | Visualization | Plotting cell populations on 2D-embeddings | Creating an expression heatmap | Displaying relationships between modules and cell populations | Examining co-expression with module heatmaps | Identifying reasonable numbers of feature modules and cell subpopulations | Using recursive splitting | Using a grid search | Miscellaneous utility functions | Finding the modules for feature with featureModuleLookup | Reordering cluster labels with recodeClusterZ, recodeClusterY | Session Information
Mutational Signature Comprehensive Analysis Toolkit1 years ago
Vignettes | Introduction | Installation | Setting up a musica object | Extracting variants | Choosing a genome | Creating a musica object | Creating mutation count tables | Creating a musica object directly from a count table | Discovering Signatures and Exposures | Determining an appropriate k value | Plotting | Signatures | Exposures | Comparison to external signatures (e.g. COSMIC) | Predicting exposures using pre-existing signatures | Comparing samples between groups using Sample Annotations | Adding sample annotations | Plotting exposures by a Sample Annotation | Visualizing samples in 2D using UMAP | Use of Plotly in plotting | Note on reproducibility | Session Information
Decontamination of single cell protein expression data with DecontPro2 years ago
Introduction | Installation | Importing data | Generate cell clusters | Run DecontPro | Plot Results | Session Information
Introduction to singleCellTK3 years ago
Vignettes | Session info