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Osmanbeyoglu Lab

Resources

Algorithms

SPaRTAN: Computational framework for linking cell-surface receptors to transcriptional regulators by exploiting CITE-seq datasets with cis-regulatory information

Link

Reference

Tutorial

CITRUS: Interpretable neural network to model the impact of somatic alterations on transcription factors and downstream transcriptional programs

Link

Reference

PSIONIC: A multitask framework that jointly models transcriptional networks for several related cancer types by leveraging chromatin accessibility and gene expression data

Link

Reference

Datasets

Mesothelioma: Human malignant mesothelioma CITE-seq profiling

Raw data

Reference

Web resources

COVID-19db of Immune Cell States: A comprehensive web resource linking surface proteins to transcription factors for host immune cell types to assist in the discovery of COVID-19 potential therapeutic targets and diagnostic biomarkers.

Web link

GitHub link

Reference

Mesothelioma Spatial Atlas: A web resource providing interactive visualizations of malignant mesothelioma multiplex immunofluorescence (mIF) dataset and eosin (H&E) images of tumor samples to facilitate the understanding of pathogenesis and identify novel therapies.

Web link

GitHub link

Reference

Tutorial

Computational Approaches for Identifying Context-Specific Transcription Factors using Single-Cell Multi-Omics Datasets

ECCB 2024

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