Gene regulatory networks (GRNs) encode the logic of cellular decision-making, with attractors representing stable cell states and feed-forward loops (FFLs) providing signal processing functions. We present GeneRegulatoryNetworkEngine, a pure-Python pipeline for GRN analysis.
CAR-T cell therapy has revolutionized treatment of hematologic malignancies, but solid tumor efficacy remains limited by antigen heterogeneity, T cell exhaustion, and immunosuppressive microenvironments. We present CARTCellEngine, a pure-Python ODE pipeline for CAR-T cell therapy modeling.
Cytokine signaling through NF-κB and JAK-STAT pathways coordinates immune responses, inflammation, and cell fate decisions. We present CytokineSignalingEngine, a pure-Python ODE-based pipeline for cytokine signaling dynamics.
Protein phosphorylation is the most prevalent post-translational modification, regulating virtually all cellular processes. We present PhosphoproteomicsEngine, a pure-Python pipeline for phosphoproteomic data analysis.
Chromatin accessibility measured by ATAC-seq reveals the regulatory landscape of the genome, identifying active enhancers, promoters, and transcription factor binding sites. We present ChromatinAccessibilityEngine, a pure-Python pipeline for ATAC-seq analysis.
Somatic copy number alterations (SCNAs) are ubiquitous in cancer, driving oncogene amplification and tumor suppressor deletion. We present CopyNumberEngine, a pure-Python pipeline for copy number analysis from whole-genome sequencing.
Protein ubiquitination is a versatile post-translational modification regulating protein degradation, DNA repair, signal transduction, and cell cycle progression. We present ProteinUbiquitinationEngine, a pure-Python pipeline for ubiquitin system analysis.
Neurogenomics integrates genomic, transcriptomic, and epigenomic data to understand brain function and neurological disease. We present NeurogenomicsEngine, a pure-Python pipeline for brain transcriptomics analysis.
Mendelian randomization (MR) uses genetic variants as instrumental variables to infer causal effects of exposures on outcomes, avoiding confounding in observational studies. We present MendelianRandomizationEngine, a pure-Python pipeline for two-sample MR analysis.
Metabolic flux analysis quantifies the flow of metabolites through biochemical reaction networks, enabling prediction of cellular metabolic phenotypes. We present MetabolicFluxEngine, a pure-Python pipeline for constraint-based metabolic modeling.
Tumors evolve through clonal expansion and diversification, generating intratumor heterogeneity that drives treatment resistance. We present ClonalEvolutionEngine, a pure-Python pipeline for tumor clonal evolution analysis from multi-region sequencing.
RNA secondary structure is critical for function, regulating translation, splicing, stability, and protein binding. We present RNAStructureEngine, a pure-Python pipeline for RNA secondary structure prediction and analysis.
MicroRNAs (miRNAs) are ~22 nt small non-coding RNAs that post-transcriptionally regulate gene expression by binding to 3'UTR seed sequences. We present MicroRNAEngine, a pure-Python pipeline for miRNA target prediction and regulatory network analysis.
Ribosome profiling (Ribo-seq) enables genome-wide measurement of translation by sequencing ribosome-protected mRNA fragments. We present RibosomeProfilingEngine, a pure-Python pipeline for Ribo-seq analysis.
Long non-coding RNAs (lncRNAs) regulate gene expression through diverse mechanisms including chromatin remodeling, transcriptional regulation, and post-transcriptional control. We present LncRNAEngine, a pure-Python pipeline for lncRNA regulatory analysis.
Circular RNAs (circRNAs) are covalently closed RNA molecules generated by back-splicing that function as miRNA sponges, protein scaffolds, and translation templates. We present CircularRNAEngine, a pure-Python pipeline for circRNA analysis.
Genome-wide CRISPR knockout screens enable systematic identification of genes essential for cellular fitness or drug response. We present CRISPRScreenEngine, a pure-Python pipeline for CRISPR screen analysis.
Enhancers are distal regulatory elements that activate gene transcription through chromatin looping, but assigning enhancers to their target genes remains challenging. We present EnhancerPromoterEngine, a pure-Python implementation of the Activity-by-Contact (ABC) model.
Histone modifications are key epigenetic regulators of gene expression, with distinct marks defining active promoters, enhancers, repressed regions, and heterochromatin. We present HistoneModificationEngine, a pure-Python pipeline for ChIP-seq histone mark analysis.
DNA methylation at CpG dinucleotides is a fundamental epigenetic mark regulating gene expression, imprinting, and X-chromosome inactivation. We present CpGMethylationEngine, a pure-Python pipeline for WGBS analysis.