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.
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.
Long-read sequencing technologies (PacBio HiFi, Oxford Nanopore) enable detection of structural variants, haplotype-resolved assembly, and repeat expansion genotyping that are inaccessible to short reads. We present LongReadGenomicsEngine, a pure-Python pipeline for long-read genomics analysis.
DNA-encoded chemical libraries (DEL) enable screening of millions of compounds simultaneously by coupling each compound to a unique DNA barcode. We present DNAEncodedLibraryEngine, a pure-Python pipeline for DEL data analysis.
Network pharmacology integrates drug-target interactions with biological networks to understand polypharmacology and identify repurposing opportunities. We present NetworkPharmacologyEngine, a pure-Python pipeline for network pharmacology analysis.
Pharmacogenomics studies how genetic variation affects drug response, enabling personalized dosing and adverse drug reaction (ADR) prevention. We present PharmacogenomicsEngine, a pure-Python pipeline for pharmacogenomics analysis.
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.
Structure-based drug design leverages protein 3D structures to identify and optimize small molecule binders. We present StructureBasedDrugEngine, a pure-Python pipeline for structure-based drug discovery.
Brain age prediction from neuroimaging data provides a biomarker of brain health, with brain age gap (BAG = predicted - chronological age) reflecting accelerated or decelerated aging. We present BrainAgeEngine, a pure-Python pipeline for brain age analysis.
Two-photon calcium imaging enables simultaneous recording of hundreds of neurons, revealing population-level neural dynamics and ensemble coding. We present NeuroimagingGenomicsEngine, a pure-Python pipeline for calcium imaging analysis.
Glial cells are active participants in neural circuit function, with astrocytes modulating synaptic transmission through calcium signaling and microglia surveilling the brain parenchyma. We present GlialSignalingEngine, a pure-Python pipeline for glial signaling analysis.
Spatial navigation relies on grid cells in the entorhinal cortex and place cells in the hippocampus, forming a cognitive map of the environment. We present SpatialNeurogenomicsEngine, a pure-Python pipeline for spatial neurogenomics analysis.