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The Zhang Lab's Projects

amp_phase1_ra icon amp_phase1_ra

Code for Zhang, Wei, Slowikowski, Fonseka, Rao, et al, Nature Immunology, 2019. Single-cell transcriptomics and proteomics data analysis and integration for rheumatoid arthritis synovial tissue. These integrative strategies can be generalized to any other diseases.

bulk_rnaseq_pipeline icon bulk_rnaseq_pipeline

Bulk RNA-seq analytical pipeline, including using Snakemake to run main steps such as Kallisto read mapping, QC, Principal Component Analysis (PCA), and other downstream analysis.

global_optimization icon global_optimization

Global optimization for mixed membership matrix factorization for omics data. Code for Zhang, et al, 2019

rvd2_variational_bayesian icon rvd2_variational_bayesian

Code for our novel Variational Bayesian method for Zhang, Flaherty, BMC Bioinformatics, 2017. This is a Python-based tool for sensitive rare variant detection for NGS data.

singlecell_functions icon singlecell_functions

We implemented and generalized single-cell functions and targeted analytical code for single-cell omics data analysis.

stew icon stew

Uncover spatially informed shared variations underlying single-cell spatial transcriptomics with STew.

ttek icon ttek

Code for Jonsson*, Zhang*, et al, TteK (Granzyme K+ CD8 T cells), Science Translational Medicine, 2022: the core population of inflamed human tissue-associated CD8 T cells.

zhang_lab_manual icon zhang_lab_manual

The Zhang Lab Manual: Lab principles and activities, Handbook for reproducible computational research, Learning resources, Expectations and achievements, etc

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