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.
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clusteringregressiontimecoursedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization
10.96 score 314 stars 962 scripts 2.1k 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.
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rnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization
6.71 score 32 stars 54 scripts 502 downloadsEcume - 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.
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softwareinfrastructure
4.98 score 1 stars 3 dependents 21 scripts 678 downloadsDune - 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.
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clusteringgeneexpressionrnaseqsoftwaresinglecelltranscriptomicsvisualization
4.65 score 45 scripts 370 downloads