zhanglabtools Goto Github PK

adc

source code for ADC

ai4or.course

Artificial Intelligence for Operations Research course

bmd-mog

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

brainalign

came

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

casava

Resources of our paper CASAVA

circlet

CIRCLET, a powerful tool for accurate reconstruction of circular trajectory with high resolution by considering multi-scale features of chromosomal architectures of single cells. Further division of the reconstructed trajectory helps to accurately characterize the dynamics of chromosomal structures and uncover important regulatory genes along cell-cycle progression, providing a novel framework for discovering regulatory regions even cancer markers at single-cell resolution.

constads

Consensus TADs

csre

The code of article "Large-scale determination and characterization of cell type-specific regulatory elements in the human genome"

dbmd

Distributed Matrix Decomposition for Big Data Mining and Clustering

deeplearningtheory.course

Deep Learning Theory course

dnadataaugmentation

Source code for paper 'Simple tricks of convolutional neural network architectures improve DNA–protein binding prediction'. In addition, some reusable code is also sort out for further use.

dsmo.course

Data Science and Matrix Optimization course

gkm-dnn

R and Scala code for calculating gapper k-mer frequency vector

hicmsd

Source code of HiCMSD

hicsrkit

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

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

mstd

MSTD is a generic and efficient method to identify multi-scale topological domains (MSTD) from symmetric Hi-C and other high resolution asymmetric promoter capture Hi-C datasets.

schi-csim

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

smartgate

stagate

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

stage

stagewisenn

Constructing developmental tree from scRNA-seq data

staligner

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

stamarker

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

twae

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