shengxinbaixiaosheng

pan-B

These are scripts for pan-cacner B cells analyses.

annosc

awesome-deep-learning-single-cell-papers

awesome_spatial_omics

tools and notes for spatial omics

BreastCancer_Integrated

fetal_lung_analysis

FME_atlas

Codes from manuscript

General_singleCell_code

Collection of generic code for analysing single cell data sets

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"

macrophage-atlas

MacrophageChemokineHeterogeneity

Code for Article "Coordinated Chemokine Expression Defines Macrophage Subsets Across Tissues"

Meta_NK_Project

Pan_Endo

RMEJLBASBMP_2024

Repository for the paper "The impact of package selection and versioning on single-cell RNA-seq analysis"

RMS-metadata

Codes for single-cell meta-data analysis of RMS

SCA-Single-Cell-Atlas-

Code Repositories for SCA

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_analysis

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

zellkonverter

Conversion between scRNA-seq objects