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.">

HetSeq: Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity (original) (raw)

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 ORCID iD [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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