Software

SC-muscle, a web-browser to explore an atlas of single-cell transcriptomic muscle datasets. The details can be found in this manuscript.

TAR-scRNA-seq is a pipeline to uncover cell-type specific unannotated transcriptional activity in single-cell RNA sequencing data. The pipeline is described in this manuscript.

HiPR-FISH (high-phylogenetic-resolution microbiome mapping by fluorescence in situ hybridization) enables automated image analysis for highly multiplexed FISH experiments on microbial communities. The details are described in this manuscript.

LBBC (Low Biomass Background Correction) is a R package to denoise metagenomic cell-free DNA sequencing data. The principles implemented in LBBC are described in this manuscript.

Protocols

DART-seq (Droplet-Assisted RNA Targeting by single-cell sequencing) is a protocol that enables simultaneous multiplexed amplicon sequencing and transcriptome analysis in single cells. More information can be found in this manuscript.

ssDNA ligation is a step-by-step protocol of the single-stranded DNA library preparation we use to sequence cell-free DNA isolated from plasma and urine. This library preparation is well suited for the recovery and DNA sequencing of ultrashort, highly fragmented cell-free DNA, as we describe in this manuscript.