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durenlab

Duren Lab website

enrichtf

genlouvain

A generalized Louvain method for community detection implemented in MATLAB

macs

MACS -- Model-based Analysis of ChIP-Seq

matlab

packagetry

PackageTry test

peca

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

peca-1

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

sc-compreg_matlab

scgeatoolbox

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

spanonmf

An algorithm for low-dimensional ONMF and multi-component NN-PCA

symnmf

Symmetric NMF for graph clustering

test

tf-activity-network

To study systems-level properties of the cell, it is necessary to go beyond individual regulators and target genes to study the regulatory network among transcription factors (TFs). However, it is difficult to directly measure TF activity or DNA-binding fraction of TF by experiment. Here, we proposed a hierarchical graphical model to estimate TF activity from mRNA expression by building TF complexes with protein co-factors and inferring TF’s downstream regulatory network simultaneously.