Code for scRNA-seq analysis of M. tuberculosis infection and CD8 depletion (Winchell et al., 2023).
Analysis code for the MIT Milk Study (single-cell analysis of human milk).
Scripts for analyses of high-fat diets priming tumorigenesis in the liver.
A framework for simultaneous in situ probing of host and microbiome across multiple spatial modalities (likely associated with the Nature paper on this topic).
Analysis tools for spatial transcriptomics, developed by lab members (e.g., Constantine Tzouanas).
Scripts for analyses of spatial analyses of multicellular neighborhoods and intercellular signaling circuits predictive of disease dysfunction in human tissue microarrays.
Uncover transcription factors that drive complex gene programs - across datasets, species, and measurement methods.
A reproducibility-driven framework for assessing expression differences and identifying conserved trends across multiple donors.
Edited SARS-CoV-2 genome FASTA and GTF files for scRNA-seq alignment (Ziegler et al., 2021).
Workflow scripts for analyzing multi-omics data (e.g., scRNA-seq + protein) generated using the Seq-Well S3 platform.
A WDL workflow for Kallisto and Bustools wrapped within kb_python.
A minor edit to the Cumulus CellRanger workflow to enable RNA+VDJ linking.
A WDL workflow for the MiXCR tool (TCR/BCR profiling).
A Python-based pipeline for identifying and quantifying Seq-Well TCR transcripts.
A workflow for aligning and processing amplicon BCR data.
Code for "Compressed phenotypic screening empowers scalable biological discovery" (Kummerlowe/Mead et al.).
Code and analyses for the manuscript "Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation" (Mead et al., Nat. Biomed. Eng., 2022).
The Alexandria Project – a single-cell portal and data resource for the global health community, including workflows and notebooks.
Materials for the Human Cell Atlas Thailand workshop.
Materials for the KEMRI-Wellcome Trust Research Programme workshop in Kilifi.
Materials for the MISTI Global Seed Fund workshop in Bogota.
