Network reconstruction algorithms

Algorithms to reconstruct regulatory networks from observed omics data, optionally using a reference network (eg, from pathway databases) as a starting point.

Time-Lagged Ordered Lasso for Network Inference

Post-PLSR: network inference using time-series data

Network analysis methods

Methods to analyze high-throughput data in the context of pathway networks (either derived from pathway databases or inferred by other means).

Evaluating network methods

GeneSurrounder

Pathway-PDM: nonlinear multi-gene analysis of gene expression data

PoDA (Pathways of Distinction Analysis)

Methods for circadian transcriptomics

Software packages to enable the optimal design and analysis of circadian gene expression data.

TimeTrial: a tool for optimizing circadian transcriptomics experiments

TimeSignature: inferring circadian phase from gene expression