tradeSeq - trajectory-based differential expression analysis for sequencing data

tradeSeq provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.

Last updated 5 months ago

clusteringregressiontimecoursedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization

10.06 score 247 stars 440 scripts 1.1k downloads

condiments - Differential Topology, Progression and Differentiation

This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an 'omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format.

Last updated 3 months ago

rnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization

6.52 score 26 stars 17 scripts 254 downloads

Ecume - Equality of 2 (or k) Continuous Univariate and Multivariate Distributions

We implement (or re-implements in R) a variety of statistical tools. They are focused on non-parametric two-sample (or k-sample) distribution comparisons in the univariate or multivariate case. See the vignette for more info.

Last updated 10 months ago

softwareinfrastructure

4.86 score 1 stars 3 dependents 16 scripts 428 downloads

Dune - Improving replicability in single-cell RNA-Seq cell type discovery

Given a set of clustering labels, Dune merges pairs of clusters to increase mean ARI between labels, improving replicability.

Last updated 5 months ago

clusteringgeneexpressionrnaseqsoftwaresinglecelltranscriptomicsvisualization

4.61 score 41 scripts 195 downloads