juzheng87's repositories
adult-human-brain
Cytograph version used for adult human-brain analysis
awesome_spatial_omics
tools and notes for spatial omics
General_singleCell_code
Collection of generic code for analysing single cell data sets
hbca
Code used to process the data of the HBCA project
HECA-Human-Endometrial-Cell-Atlas
Human Endometrial Cell Atlas (HECA). An integrated single-cell reference atlas of the human endometrium.
Human_fetal_lung_atlas
Code available for: Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity (Quach & Farrell, et al.)
HumanColonCancer_VisiumHD
Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"
ircolitis
Analysis of single-cell RNA-seq data from patients with immunotherapy-related colitis.
MacrophageChemokineHeterogeneity
Code for Article "Coordinated Chemokine Expression Defines Macrophage Subsets Across Tissues"
RMEJLBASBMP_2024
Repository for the paper "The impact of package selection and versioning on single-cell RNA-seq analysis"
scBreast_scRNA_scATAC_2024
Repository to store code used for the analyses presented in "Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic And Transcriptome Profiling"
sccomp
Testing differences in cell type proportions from single-cell data.
scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
Single-cell-atlas-of-the-human-brain-vasculature-accross-development-adulthood-and-disease
Molecular atlas of the human brain vasculature accross development, adulthood and disease at the single-cell level
spatial-bonemarrow-atlas
This repository contains the code used to generate figures and perform analysis for the manuscript titled "Transcriptomic and Spatial Proteomic Profiling Reveals the Cellular Composition and Spatial Organization of the Human Bone Marrow Microenvironment"
Spatial_Glioma
Code for major analyses in "Integrative spatial analysis reveals a multi-layered organization of glioblastoma" paper
spatialDLPFC
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
starfysh
Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology
Stereopy
A toolkit of spatial transcriptomic analysis.
TCAT_analysis
Code repository for TCAT analyses