Results for “computational-pathology”

Analyze whole-slide pathology images with Python: load 160+ slide formats, preprocess H&E stains, segment nuclei, construct spatial graphs, train ML models, and process multiplex immunofluorescence data (CODEX, Vectra).

Process whole slide images for digital pathology: detect tissue, extract tiles, and prepare datasets for deep learning pipelines.

Build clinical deep-learning pipelines with PyHealth: load EHR, signal, and imaging datasets, define prediction tasks, instantiate models, train with the PyHealth Trainer, and compute clinical metrics.

Diagnose and observe an Oxla distributed analytical database using system catalog tables, Prometheus metrics, runtime log-level changes, and troubleshooting workflows for slow queries, node health, and memory/OOM pressure. Also covers debugging Oxla's external data sources, including the Redpanda/Kafka ingestion path.

Analyze PCAP files by reconstructing TCP/UDP sessions, decoding application-layer protocols, and correlating packet sequences with host or malware behavior for CTF challenges.

Perform fast genomic interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps), multi-format bioinformatics I/O, DataFusion SQL, and pileup on Polars DataFrames via the polars-bio library, serving as a scalable alternative to bioframe and bedtools.

Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data. Use when asked how often a gene is mutated/amplified/deleted in a tumor type, to profile oncogenes or tumor suppressors across cancers (pan-cancer alteration frequency), to pull patient-level mutations joined to OS/clinical outcomes, or to validate a cancer target from cohort genomics. For germline variant pathogenicity use alterlab-clinvar; for mutational-signature (SBS) decomposition use alterlab-cosmic; for CRISPR/RNAi gene-dependency use alterlab-depmap; for aggregated target-disease evidence use alterlab-opentargets. Part of the AlterLab Academic Skills suite.