We describe Damselfly, A permutation-based paired-AUC comparison tuned for small and label-sparse clinical datasets where DeLong's normal approximation is unreliable.. The DeLong test is standard for comparing two AUCs on the same samples but relies on a normal approximation of the covariance of U-statistics that fails at small sample size or when the positive class is severely imbalanced.
Alpha diversity is the most frequently reported summary statistic in gut microbiome case-control studies, yet the choice among competing indices is rarely justified and the consequences of that choice for biological conclusions are seldom examined. We reanalyzed 16S rRNA amplicon data from 14 published gut microbiome datasets spanning seven disease categories (obesity, type 2 diabetes, inflammatory bowel disease, colorectal cancer, Clostridium difficile infection, cirrhosis, and rheumatoid arthritis), computing five standard alpha diversity indices (Shannon, Simpson, Chao1, observed OTUs, and Faith's phylogenetic diversity) for each.
Six global atmospheric reanalysis products -- ERA5, JRA-55, MERRA-2, NCEP-R2, CFSR, and the Twentieth Century Reanalysis (20CR) -- serve as the observational backbone for climate trend attribution, yet their mutual consistency has never been audited at the grid-cell level with formal uncertainty quantification. We extract monthly 850 hPa temperature fields from all six products on a common 2.
The additivity assumption — that the potency effects of two independent structural modifications combine linearly — underpins free energy perturbation calculations, multi-parameter QSAR, and routine medicinal chemistry extrapolation. We test this assumption using matched molecular pair (MMP) squares across nine ChEMBL targets spanning five therapeutic target families, with a dual-null permutation framework that separates two distinct claims.
GC-content bias in microarray and RNA-seq platforms is well-documented but rarely corrected in differential expression analyses. We audit 20 widely-cited microarray datasets from GEO, applying a permutation-based test that evaluates whether the overlap between differentially expressed gene lists and GC-content-correlated genes exceeds chance.
Endometriosis affects approximately 10% of reproductive-age women, yet no validated transcriptomic biomarker has reached clinical use. A persistent obstacle is that publicly available microarray datasets—widely cited in biomarker discovery—differ not only in sample size and patient population but in the tissue compartments they compare.
Endometriosis affects ~10%% of reproductive-age women yet averages 6.6 years to diagnose.
The standard genetic code places amino acids on codons in a pattern that has long been interpreted as minimizing the impact of point mutations on protein function. Prior analyses differ in which amino acid properties they test, which random code ensemble they use as a null distribution, and whether they account for realistic mutation biases.