Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity R package HetSeq version 0.1.1 Cellular responses to perturbations are highly heterogeneous and depend largely on the initial state of cells. Connecting post-perturbation cells via cellular trajectories to untreated cells (e.g. by leveraging metabolic labeling information) enables exploitation of intercellular heterogeneity as a combined knock-down and overexpression screen to identify pathway modulators, termed Heterogeneity-seq (see 'Berg et al' <doi:10.1101/2024.10.28.620481>). This package contains functions to generate cellular trajectories based on scSLAM-seq (single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing) time courses, functions to identify pathway modulators and to visualize the results. Software Depends: R (>= 4.1.0) Imports: cowplot, doParallel, foreach, DoubleML, e1071, igraph, ggplot2, ggrastr, ggrepel, grandR, lpSolve, mlr3, pROC, reshape2, scales, Seurat, stats Kevin Berg <Kevin.Berg@informatik.uni-regensburg.de> Comprehensive R Archive Network (CRAN) Kevin Berg [aut, cre], Florian Erhard [aut] (ORCID: <https://orcid.org/0000-0002-3574-6983>), Lygeri Sakellaridi [aut] Apache License (>= 2) 2026-06-01 application/tgz https://CRAN.R-project.org/package=HetSeq doi:10.32614/CRAN.package.HetSeq