The Zhang Lab

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14 repositories

Zhang_lab_manual
Public
The Zhang Lab Manual: Lab principles and activities, Handbook for reproducible computational research, Learning resources, Expectations and achievements, etc
reproducible-research computational-biology bioinformatics-resources computational-lab-manual
2•3•0•0•Updated Dec 9, 2024Dec 9, 2024
SCRNA-GWAS-Benchmarking
Public
This repository contains the work/pipeline done to prepare GWAS summary statistics, run MAGMA, scGWAS, and scDRS for ...
Jupyter Notebook
•0•1•0•0•Updated Dec 5, 2024Dec 5, 2024
STew
Public
Uncover spatially informed variations underlying single-cell spatial transcriptomics with STew.
HTML
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MIT License
•1•7•0•0•Updated May 31, 2024May 31, 2024
wall-of-software
Public
A list of tools, packages, workflows, resources, and other software developed at or in collaboration with DBMI
HTML
•8•0•0•0•Updated Feb 28, 2024Feb 28, 2024
singlecell_functions
Public
We implemented and generalized single-cell functions and targeted analytical code for single-cell omics data analysis.
python machine-learning r functions statistical-models omics-analysis visualization single-cell
Jupyter Notebook
•2•1•0•0•Updated Nov 2, 2023Nov 2, 2023
singlecell_preprocessing
Public
Single-cell preprocessing pipelines, such as converting raw bcl files, make fastqs and then generating quantified matrix, etc
bash-script snakemake-workflows 10x-genomics kallisto-bustools
Jupyter Notebook
•0•0•0•0•Updated Nov 1, 2023Nov 1, 2023
AtRiskRA_SingleCell
Public
Source code for the At-Risk RA work
computational-biology translationalscience single-cell-omics cytof-data autoimmune-disease systems-immunology
Jupyter Notebook
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MIT License
•1•0•0•0•Updated Jul 7, 2023Jul 7, 2023
rvd2_variational_bayesian
Public
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.
python next-generation-sequencing variant-calling variational-bayes-inference
Python
•0•1•0•0•Updated Oct 20, 2022Oct 20, 2022
amp_phase1_ra
Public
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.
r omics-data-integration immunogenomics autoimmune-disease single-cell
Jupyter Notebook
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GNU General Public License v3.0
•0•0•0•0•Updated Jul 2, 2022Jul 2, 2022
inflamedtissue_covid19_reference
Public
Code for Zhang, et al, Genome Medicine, 2021. Cross-disease tissue data integration on single-cell transcriptomics
single-cell-rna-seq batch-correction metadata-analysis tissue-infammation disease-association-testing
Jupyter Notebook
•0•1•0•0•Updated Jul 2, 2022Jul 2, 2022
TteK
Public
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.
tcr-repertoire immunogenomics tcell single-cell-omics inflammation rheumatoid-arthritis
Jupyter Notebook
•0•0•0•0•Updated Jul 1, 2022Jul 1, 2022
bayesian_r
Public
Bayesian modeling and inference in R
r bayesian-inference
Jupyter Notebook
•0•0•0•0•Updated Jun 14, 2022Jun 14, 2022
global_optimization
Public
Global optimization for mixed membership matrix factorization for omics data. Code for Zhang, et al, 2019
python machine-learning matrix-factorization algorithm optimization
Python
•0•0•0•0•Updated Feb 16, 2022Feb 16, 2022
bulk_RNAseq_pipeline
Public
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.
kallisto snakemake-workflows bulk-rna-seq
HTML
•0•0•0•0•Updated Feb 16, 2022Feb 16, 2022