Protocols

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.

STRS (Spatial Total RNA-Sequencing) is a method to spatially map the total transcriptome – including coding RNAs, noncoding RNAs, and viral/microbial RNAs. More information can be found in this manuscript. Also check out our pipeline for alignment and quantification of STRS data on github.

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. Find the original code here, and a lighter version of the pipeline here.

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.

Software

scMuscle, a web-browser to explore an atlas of single-cell transcriptomic muscle datasets. The details can be found in this manuscript. Check out the updated version of this work, scMuscle2, on github!

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.

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.