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 …
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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 …
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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 …
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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. …
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