Fig. 1: General workflow and analysis schema of PALMO.

a PALMO can work with complex longitudinal data, including clinical data, bulk omics data, and single-cell omics data. b Overview of five analytical modules implemented in PALMO. c Variance decomposition analysis (VDA) applies generalized linear mixed model to assess contributions of factors of interest (such as disease status, sex, individual participant, cell type, experimental batch, etc.) to the total variance of individual features in the data. d Coefficient of variation (CV) profiling (CVP) is designed for bulk longitudinal data, calculates CV of repeated measurements on the same participant to assess the corresponding longitudinal stability, and compares CVs of different participants to identify consistently stable or variable features. e Stability pattern evaluation across cell types (SPECT) is the CVP counterpart for single-cell omics data, analyzes stability patterns of features across different cell types and different participants, classifies features based on how often they are stable or variable in cell type-donor combinations, and identifies features that are unique to individual cell types and consistent among participants. f Outlier detection analysis (ODA) evaluates how many features in a sample are outliers when compared with the corresponding features in other samples of same participant, assesses whether the number of outlier features in the sample is significantly higher than expectation, and identifies possible abnormal events occurred during a longitudinal study. g Time course analysis (TCA) uses the hurdle model to evaluate transcriptomic changes over time based on longitudinal scRNA-seq data of same participants, models time as a continuous variable for data with at least three timepoints, and identifies up- or down-regulated genes over time. h PALMO uses circos plots to display CVs of features of interest and reveal stability patterns across features, participants, cell types, and data modalities. Adobe Illustrator (version 27.1.1; https://www.adobe.com/products/illustrator.html) was used to draw (a), arrange panels, and edit text. PowerPoint (version 16.69; https://www.microsoft.com/en-us/microsoft-365/powerpoint) was used to draw (b).