The Drosophila melanogaster gap genes circuit simulator, coupled with Scatter Search optimization algorithm

CREST-seq peak calling.

Integrated workflow to predict super-enhancers and compute feature importance

An R package for multi-dimensional pathway enrichment analysis (legacy repo)

target: An R Package to Predict Combined Function of Transcription Factors

An integrative toolkit for detecting cell type-specific regulators

simulating dysregulated gene expression in single cell transcriptome data

enabling pathway analysis of curated chip-seq data

A resource of gene expression signatures derived from the DEE2 dataset (http://dee2.io)

Source code for miRiam web server and visualisation

A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.

Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"

Source code for JASPAR web portal and REST API

Research compendium for the preprint "Hierarchical Regulation of Autophagy During Adipocyte Differentiation"

Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks

Analysis of regulatory impacts of autism-associated SNPs on biological pathways in the fetal and adult cortex.

Gene Regulation Application Ontology

Crosstalk between codon optimality and 3' UTR cis-elements dictates mRNA stability

R package to predict gene feed forward loops using mediation analysis. Analyses integrate observed miRNA and mRNA expression data and database information on gene interactions.

Predict small molecule-mediated regulatory effects on miRNA expression