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The bias in mutation burden due to copy number alterations
Somatic copy number aberrations (SCNAs) — gains or losses of regions of DNA due to chromosomal instability and structural variations — are prevasive in cancer...
Modeling the between-tumor genomic divergence
Here we give a snapshot of our recently published paper “Elements and evolutionary determinants of genomic divergence between paired primary and metastatic tumors” in PLoS...
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The bias in mutation burden due to copy number alterations
Somatic copy number aberrations (SCNAs) — gains or losses of regions of DNA due to chromosomal instability and structural variations — are prevasive in cancer genomes. High overall ploidy are...
Modeling the between-tumor genomic divergence
Here we give a snapshot of our recently published paper “Elements and evolutionary determinants of genomic divergence between paired primary and metastatic tumors” in PLoS Computational Biology.
Mirrored histogram for comparing pairwise VAF Distributions among multiple tumor samples
The idea in comparing VAF histograms above and below the axis for two samples was originally from Andrea Sottoriva, and I have made improvements on coloring the cloncal status of...
Plotting the inequality of sequencing coverage
Inequality in sequencing coverage is a key factor that will lead to biases in variant detection and measurement of genomic diversity. Hence it will be beneficial to quantify the extent...
Use UpSetR to show overlaps among sets
Thinking about plotting the intersections between multiple sets? Stop using venndiagram and try UpSetR. There are lots of powerful things you can do with it. For example, here I am...
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