ithgraphy
Visualizing Tumor Heterogeneity and Genomic Sequencing Data, memo of thoughts.
Category RNA-Seq
The term “coverage” for a gene in an RNA-seq experiment can be viewed in two ways. The first is the overall number of reads (depth of coverage) that are mapped...
Category pairwise comparison
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...
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...
Category detection bias
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...
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.
Hand drawing from Athanasios N. Nikolakopoulos
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...
Category ssnv
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...
Category modeling
Hand drawing from Athanasios N. Nikolakopoulos
Category clonal dynamics
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...
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.
Category mathematical modeling
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...
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.
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