Algorithms

Using predictive specificity to determine when gene set analysis is biologically meaningful

Gene set analysis, which translates gene lists into enriched functions, is among the most common bioinformatic methods. Yet few would advocate taking the results at face value. Not only is there no agreement on the algorithms themselves, there is no …

Positive and negative forms of replicability in gene network analysis

MOTIVATION: Gene networks have become a central tool in the analysis of genomic data but are widely regarded as hard to interpret. This has motivated a great deal of comparative evaluation and research into best practices. We explore the possibility …

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

MOTIVATION: RNA-seq co-expression analysis is in its infancy and reasonable practices remain poorly defined. We assessed a variety of RNA-seq expression data to determine factors affecting functional connectivity and topology in co-expression …

Measuring the wisdom of the crowds in network-based gene function inference

MOTIVATION: Network-based gene function inference methods have proliferated in recent years, but measurable progress remains elusive. We wished to better explore performance trends by controlling data and algorithm implementation, with a particular …