A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
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Updated
Apr 5, 2024 - Jupyter Notebook
A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
Detecting Regulatory Elements using GRO-seq and PRO-seq
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks
Code and data used to create the JASPAR UCSC Genome Browser tracks data hub
A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.
Fast Inference of Networks from Directed Regulations
An R package for multi-dimensional pathway enrichment analysis
Analysis and retrieval of Regulatory EleMents (REMs) linked to genes
Association analysis of ADH and ALDH gene regulatory interactions with GWAS traits.
Meta-analysis of DNA methylation in ART
De novo discovery of traits co-occurring with chronic obstructive pulmonary disease.
Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data
Crosstalk between codon optimality and 3' UTR cis-elements dictates mRNA stability
Code for the research article "Exploring functional protein covariation across single cells using nPOP". It is distributed under MIT license.
Source code for miRiam web server and visualisation
Code and data used by the JASPAR profile inference tool
pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs
Analysis of regulatory impacts of autism-associated SNPs on biological pathways in the fetal and adult cortex.
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