Ferroptosis is an iron-dependent form of regulated cell death driven by lipid peroxidation, distinct from apoptosis and necroptosis. We present FerroptosisEngine, a pure-Python pipeline for ferroptosis analysis integrating transcriptomics, lipidomics, and iron metabolism modeling.
The human microbiome plays critical roles in health and disease, with dysbiosis associated with inflammatory bowel disease, obesity, and cancer. We present MicrobiomeEngine, a pure-Python pipeline for 16S rRNA amplicon and metagenomic analysis.
Three-dimensional genome organization plays a fundamental role in gene regulation through topologically associating domains (TADs), chromatin loops, and A/B compartments. We present ChromatinConformationEngine, a pure-Python pipeline for Hi-C data analysis.
Liquid biopsy through circulating tumor DNA (ctDNA) analysis enables non-invasive cancer detection and monitoring. We present LiquidBiopsyEngine, a pure-Python pipeline for comprehensive cfDNA analysis.
N6-methyladenosine (m6A) is the most abundant internal mRNA modification, regulating splicing, translation, and decay. We present EpitranscriptomicsEngine, a pure-Python pipeline for m6A analysis from MeRIP-seq data.
Structural variants (SVs) — deletions, duplications, inversions, translocations, and insertions — are major drivers of cancer and genetic disease. We present StructuralVariantEngine, a pure-Python pipeline for SV detection and analysis.
Single-cell multi-omics simultaneously profiles gene expression and chromatin accessibility, enabling unprecedented resolution of gene regulatory programs. We present SingleCellMultiomeEngine, a pure-Python pipeline for joint scRNA-seq and scATAC-seq analysis.
Computational molecular docking is central to structure-based drug discovery. We present MolecularDockingEngine, a pure-Python virtual screening pipeline implementing: (1) geometric binding pocket detection using probe sphere rolling; (2) ligand conformer generation with rotatable bond sampling; (3) a multi-term scoring function combining van der Waals (Lennard-Jones 6-12), electrostatics (Coulomb), hydrogen bonding, and desolvation terms; (4) virtual screening of 200-compound libraries; and (5) ADMET filtering (Lipinski + TPSA + rotatable bonds).
Tumor immune evasion is a major barrier to immunotherapy. We present ImmuneEvasionEngine, a pure-Python pipeline for comprehensive tumor immune evasion analysis.
Cellular senescence is a fundamental biological process implicated in aging, cancer, and tissue homeostasis. We present SenescenceEngine, a pure-Python pipeline for comprehensive single-cell senescence analysis.
Drug combination therapy is central to cancer and infectious disease treatment. We present DrugSynergyEngine, a pure-Python pipeline implementing Hill equation fitting (mean R²=0.
Fusion genes from chromosomal rearrangements are key cancer drivers (BCR-ABL1, EML4-ALK). We present FusionGeneEngine, a pure-Python pipeline for fusion detection from RNA-seq via split-read/discordant pair filtering, in-frame prediction, domain disruption scoring, and oncogenic scoring against a 20-fusion COSMIC-style database.
Polygenic risk scores (PRS) aggregate thousands of genetic variants to predict complex disease risk. We present PolygenicRiskEngine, a pure-Python C+T PRS pipeline implementing LD clumping (r2<0.
Alternative splicing affects over 95% of multi-exon human genes and is dysregulated in cancer and neurodegeneration. We present SplicingEngine, a pure-Python pipeline implementing PSI quantification for five event types, differential splicing detection (t-test + Fisher's exact + BH FDR), and RNA-binding protein motif enrichment for 15 canonical RBPs.
We present ProteomicsEngine, a fully executable pure-Python pipeline for data-dependent acquisition (DDA) shotgun proteomics analysis. ProteomicsEngine implements four core computational modules: (1) peptide identification scoring using an Andromeda-inspired hyperscore; (2) protein inference via the parsimony principle; (3) label-free quantification using MaxLFQ-style intensity normalization; and (4) differential protein abundance testing with BH FDR correction.
Drug resistance mutations alter protein structure to reduce drug binding while maintaining protein function, posing a major challenge in cancer and infectious disease treatment. We present DrugResistanceEngine, a pure-Python pipeline for drug resistance analysis.
Stem cell genomics characterizes pluripotency states, differentiation trajectories, and reprogramming efficiency using transcriptomic and epigenomic signatures. We present StemCellGenomicsEngine, a pure-Python pipeline for stem cell genomics analysis.
Adeno-associated virus (AAV) vectors are the leading gene therapy delivery platform, with different serotypes showing distinct tissue tropism. We present GeneTherapyEngine, a pure-Python pipeline for gene therapy analysis.
Alternative polyadenylation (APA) generates transcript isoforms with different 3'UTR lengths, affecting mRNA stability, localization, and translation. We present AlternativePolyadenylationEngine, a pure-Python pipeline for APA analysis.
Clinical variant interpretation requires systematic application of ACMG/AMP guidelines to classify variants as pathogenic, likely pathogenic, VUS, likely benign, or benign. We present VariantInterpretationEngine, a pure-Python pipeline for variant interpretation.