DNA Copy Number Analysis for Genome-Wide Tapestri Panels
Generate a box plot from assay data
Generate heatmap of assay data
Calculate relative copy number value for each cell-probe unit using re...
Call copy number for each cell-chromosome using Gaussian mixture model...
Normalize raw counts
Smooth copy number values across chromosomes and chromosome arms
Call sample labels based on feature counts
Print the top-left corner of a matrix
Get read counts from barcoded reads
Create TapestriExperiment object from Tapestri Pipeline output
Get chromosome order from a string of chromosome/contig names
Add chromosome cytobands and chromosome arms to TapestriExperiment
Calculate decision boundaries between components of copy number GMMs
Get tidy-style data from TapestriExperiment objects
karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels
Move non-genome probes counts and metadata to altExp slots
Create Example TapestriExperiment
Plot of PCA proportion of variance explained
Plot copy number GMM components
Scatter plot for dimensional reduction results
Cluster 2D data
Cluster assay data by Principal Components Analysis
Cluster matrix data by UMAP
Getter and Setter functions for TapestriExperiment slots
TapestriExperiment Class Definition
Analysis of DNA copy number in single cells using custom genome-wide targeted DNA sequencing panels for the Mission Bio Tapestri platform. Users can easily parse, manipulate, and visualize datasets produced from the automated 'Tapestri Pipeline', with support for normalization, clustering, and copy number calling. Functions are also available to deconvolute multiplexed samples by genotype and parsing barcoded reads from exogenous lentiviral constructs.
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