zhanglabtools

DSMO.course

Data Science and Matrix Optimization course

STAGATE

Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics

DeepLearningTheory.course

Deep Learning Theory course

STAligner

STAligner: Integrating spatial transcriptomics data across different conditions, technologies, and developmental stages

BrainAlign

STAGE

AI4OR.course

Artificial Intelligence for Operations Research course

CAME

Cell-type Assignment and Module Extraction based on a heterogeneous graph neural network.

ConsTADs

Consensus TADs

scHi-CSim

scHi-CSim, a simulator for generating single-cell Hi-C data.

stagewiseNN

Constructing developmental tree from scRNA-seq data

STAMarker

STAMarker: Identify Spatial Domain-specific Variable Genes via Ensemble Graph Attention Autoencoders

ADC

source code for ADC

dbmd

Distributed Matrix Decomposition for Big Data Mining and Clustering

ImputeHiFI

ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single-Cell Hi-C and RNA FISH Data

STALocator

STAMapper

TADGATE

TADGATE is a computational tool to identify TADs in Hi-C contact map with a graph attention autoencoder.

CASAVA

Resources of our paper CASAVA

HiCMSD

Source code of HiCMSD

Mactop

deciphering chromatin domain, domain community and chromunity for 3D genome maps

MN-PCA

Matrix normal PCA for interpretable dimension reduction and graphical noise modeling

SmartGate

STADIA

BMD-MoG

The code file for paper BMD-MoG. main file: BMD_MoG.m

CAMEX

hicsrkit

A package used to enhance Hi-C maps with deep learning

STABox

Interactive analysis and visualization of spatial transcriptome GUI program

STASCAN

TWAE

A non-adversarial generative autoencoder with divide-and-conquer strategy