4 papers
Sashimi plots: Quantitative visualization of RNA sequencing read alignments
Yarden Katz, Eric T. Wang, Jacob Silterra +5
We introduce Sashimi plots, a quantitative multi-sample visualization of mRNA sequencing reads aligned to gene annotations. Sashimi plots are made using alignments (stored in the S…
Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data
Saumyadipta Pyne, Kui Wang, Jonathan Irish +10
In systems biomedicine, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multi-variable…
Compression of structured high-throughput sequencing data
Fabien Campagne, Kevin C. Dorff, Nyasha Chambwe +3
Large biological datasets are being produced at a rapid pace and create substantial storage challenges, particularly in the domain of high-throughput sequencing (HTS). Most approac…
The Limitations of Simple Gene Set Enrichment Analysis Assuming Gene Independence
Pablo Tamayo, George Steinhardt, Arthur Liberzon +1
Since its first publication in 2003, the Gene Set Enrichment Analysis (GSEA) method, based on the Kolmogorov-Smirnov statistic, has been heavily used, modified, and also questioned…