No packages match

grandR - Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Nucleotide conversion sequencing experiments have been developed to add a temporal dimension to RNA-seq and single-cell RNA-seq. Such experiments require specialized tools for primary processing such as GRAND-SLAM, (see 'Jürges et al' <doi:10.1093/bioinformatics/bty256>) and specialized tools for downstream analyses. 'grandR' provides a comprehensive toolbox for quality control, kinetic modeling, differential gene expression analysis and visualization of such data. Fast Wilcoxon tests are supported via the 'presto' package (available at https://github.com/immunogenomics/presto).

Last updated

6.33 score 17 stars 1 dependents 21 scripts 258 downloads

lfc - Log Fold Change Distribution Tools for Working with Ratios of Counts

Ratios of count data such as obtained from RNA-seq are modelled using Bayesian statistics to derive posteriors for effects sizes. This approach is described in Erhard & Zimmer (2015) <doi:10.1093/nar/gkv696> and Erhard (2018) <doi:10.1093/bioinformatics/bty471>.

Last updated

bayesiantranscriptomicsdifferentialexpression

5.32 score 7 stars 2 dependents 5 scripts 181 downloads

HetSeq - Identifying Modulators of Cellular Responses Leveraging Intercellular 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.

Last updated

2.70 score 3 scripts 134 downloads