shengxinbaixiaosheng

pan-B

These are scripts for pan-cacner B cells analyses.

annosc

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

Pan_Endo

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"

zellkonverter

Conversion between scRNA-seq objects

sccomp

Testing differences in cell type proportions from single-cell data.

HumanColonCancer_VisiumHD

Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"

RMS-metadata

Codes for single-cell meta-data analysis of RMS

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

Human_fetal_lung_atlas

Code available for: Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity (Quach & Farrell, et al.)

fetal_lung_analysis

macrophage-atlas

General_singleCell_code

Collection of generic code for analysing single cell data sets

Meta_NK_Project

HECA-Human-Endometrial-Cell-Atlas

Human Endometrial Cell Atlas (HECA). An integrated single-cell reference atlas of the human endometrium.

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"

TCAT_analysis

Code repository for TCAT analyses

MacrophageChemokineHeterogeneity

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

Spatial_analysis

Stereopy

A toolkit of spatial transcriptomic analysis.

DiffSided_CRC_SCseq

awesome-deep-learning-single-cell-papers

FME_atlas

Codes from manuscript

SC-AgeSpePCa

Single-cell analysis identify the age-associated divergent microenvironments and progression patterns in prostate cancer

BreastCancer_Integrated

starfysh

Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology

RMEJLBASBMP_2024

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

SCA-Single-Cell-Atlas-

Code Repositories for SCA