wmacnair

psupertime

psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels

SampleQC

Robust, multivariate, multi-sample, multi-celltype QC for single cell RNA-seq data

psupplementary

Supplementary data and analyses for the package psupertime

TreeTop

TreeTop is an algorithm for single-cell data analysis to identify and assess statistical significance of branch points in biological processes with possibly multi-level branching hierarchies. We demonstrate branch point identification for processes with varying topologies, including T cell maturation, B cell differentiation and hematopoiesis. Our analyses are consistent with recent experimental studies suggesting a shallow hierarchy of differentiation events in hematopoiesis, rather than the classical multi-level hierarchy.

muscat

Multi-sample multi-group scRNA-seq analysis tools

TreeTop_data

Example data for package TreeTop

popalign

SampleQC_paper_analyses

workflowR website for SampleQC paper analyses