Technology
Code for Analyzing Single-Cell RNA-seq Data
GitHub Repositories:
- Single-Cell Hierarchical Poisson Factorization (scHPF)
- Pipeline for clustering and differential expression analysis
- scRNA-Seq with on-chip reverse transcription
- scRNA-Seq with off-chip reverse transcription
- Mold design for microwell arrays on 6 inch silicon wafer
- Mold design for flow cell on 6 inch silicon wafer
Publications: Levitin et al, Molecular Systems Biology, 2019.
Single-Cell RNA-Seq in Microwells
Protocols:
Publications: Yuan and Sims, Scientific Reports, 2016; Bose et al, Genome Biology, 2015.
PLATE-Seq
Protocol: PLATE-Seq Protocol
Publications: Bush, Ray et al, Nature Communications, 2017.
Low-Input RNA-Seq with LNA Capture and Template-Switching
Protocol: Low-Input RNA-Seq Protocol
Publications: Pulko et al, Nature Immunology, 2016; Pan et al, Oncotarget, 2017.
Ligation-Free Ribosome Profiling
Protocol: Ligation-Free Ribosome Profiling Protocol
Publications: Hornstein, Torres et al, Genome Biology, 2016.
DEFND-seq
Protocol: DEFND-seq Protocol
Publications: Olsen et al, bioRxiv, 2023.