HetSeq: Identifying Modulators of Cellular Responses LeveragingIntercellular Heterogeneity
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.
| Version: | 0.1.0 |
| Depends: | R (≥ 4.1.0) |
| Imports: | cowplot,doParallel,foreach,DoubleML,e1071,igraph,ggplot2,ggrastr,ggrepel,grandR,lpSolve,mlr3,pROC,reshape2,scales,Seurat, stats |
| Published: | 2025-02-03 |
| DOI: | 10.32614/CRAN.package.HetSeq |
| Author: | Kevin Berg [aut, cre], Florian Erhard [aut], Lygeri Sakellaridi [aut] |
| Maintainer: | Kevin Berg <Kevin.Berg at informatik.uni-regensburg.de> |
| BugReports: | https://github.com/erhard-lab/HetSeq/issues |
| License: | Apache License (≥ 2) |
| URL: | https://github.com/erhard-lab/HetSeq |
| NeedsCompilation: | no |
| Materials: | README,NEWS |
| CRAN checks: | HetSeq results |
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