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.
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Updated
Jun 8, 2022 - R
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.
CREST-seq peak calling.
A resource of gene expression signatures derived from the DEE2 dataset (http://dee2.io)
An integrative toolkit for detecting cell type-specific regulators
simulating dysregulated gene expression in single cell transcriptome data
All code generated from Rogers et al. 2024
Gene regulation exploring with OOP
Research compendium for the preprint "Hierarchical Regulation of Autophagy During Adipocyte Differentiation"
ChIP-seq analysis pipeline encompassing data processing, quality control, alignment, peak calling, annotation and motif analysis.
The Drosophila melanogaster gap genes circuit simulator, coupled with Scatter Search optimization algorithm
enabling pathway analysis of curated chip-seq data
Inferring ncRNA synergistic competition
A powerful abstraction of gene databases
Code for simulations and analysis used in Menon et al., 2024, "Proximal termination generates a transcriptional state that determines the rate of establishment of Polycomb silencing "
An R package for multi-dimensional pathway enrichment analysis (legacy repo)
All code generated for Loupe et al. 2023
Predict small molecule-mediated regulatory effects on miRNA expression
Depicting pseudotime-lagged causality for accurate gene-regulatory inference
Python visualization of single locus SMF data
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