Single-cell Variational Inference (scVI)
Single-cell Variational Inference (scVI) uses a deep generative model to analyze single-cell RNA sequencing datasets Learn More
FastProject uses gene sets to analyze low-dimensional projections of single-cell RNAseq expression data. Learn More
ImpulseDE2 and ImpulseDE
ImpulseDE2 and ImpulseDE use a single-impulse functional model to identify genes that are differentially expressed in a single time course (across time) or between two time courses. Find out more
SCONE (Single-Cell Overview of Normalized Expression): An R Package for QC and Normalization of single cell RNA-Seq Data. Read more
scRAD (Single-Cell Reproducibility Across Donors) supports a reproducibility-driven framework for assessing expression differences in single-cell RNA-Seq (scRNA-Seq) data collected from multiple donors. Read more here
TRAPeS (TCR Reconstruction Algorithm for Paired-End Single-cell): a Python/ C++ package for efficiently extracting T cell receptor sequences from standard, short-read single cell RNA-seq libraries. Download it here.