The Zhang Lab
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18 repositories
scLASER
PublicscLASER: Single-Cell Longitudinal Simulation and Time-Dependent Association DetectionZhang_lab_manual
PublicThe Zhang Lab Manual: Lab principles and activities, handbook for reproducible computational research, learning resources, expectations and achievements, etcwall-of-software
PublicSTEAM
PublicpyCellPhenoX
PublicSCORPIO
PublicAtRiskRA_SingleCell
PublicSource code for the At-Risk RA worksinglecell_functions
PublicWe implemented and generalized single-cell functions and targeted analytical code for single-cell omics data analysis.SCRNA-GWAS-Benchmarking
PublicSTew
Publicsinglecell_preprocessing
PublicSingle-cell preprocessing pipelines, such as converting raw bcl files, make fastqs and then generating quantified matrix, etc- Code for our novel Variational Bayesian method for Zhang, Flaherty, BMC Bioinformatics, 2017. This is a Python-based tool for sensitive rare variant detection …
amp_phase1_ra
PublicCode for Zhang, Wei, Slowikowski, Fonseka, Rao, et al, Nature Immunology, 2019. Single-cell transcriptomics and proteomics data analysis and integration for rhe…- Code for Zhang, et al, Genome Medicine, 2021. Cross-disease tissue data integration on single-cell transcriptomics
TteK
PublicCode for Jonsson*, Zhang*, et al, TteK (Granzyme K+ CD8 T cells), Science Translational Medicine, 2022: the core population of inflamed human tissue-associated …bayesian_r
PublicBayesian modeling and inference in Rglobal_optimization
PublicGlobal optimization for mixed membership matrix factorization for omics data. Code for Zhang, et al, 2019bulk_RNAseq_pipeline
PublicBulk RNA-seq analytical pipeline, including using Snakemake to run main steps such as Kallisto read mapping, QC, Principal Component Analysis (PCA), and other d…
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