Results for “scikit-bio”

Perform survival analysis and time-to-event modeling in Python using scikit-survival, including Cox models, random survival forests, gradient boosting, survival SVMs, and evaluation metrics like concordance index and Brier score.

Process and analyze physiological signals including ECG, EEG, EDA, RSP, PPG, EMG, and EOG using Python.

Provides guidance for using RDKit to read and write molecular structures, calculate descriptors, generate fingerprints, perform substructure searches, and handle chemical reactions.

Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling. Use when custom sanitization, specialized fingerprint or descriptor algorithms, reaction enumeration, or conformer generation demand direct API control; for a high-level pandas-friendly wrapper over RDKit prefer alterlab-datamol, and for turning molecules into ML feature vectors prefer alterlab-molfeat. Part of the AlterLab Academic Skills suite.

Perform cheminformatics tasks including molecular I/O, descriptor calculation, fingerprinting, substructure search, and similarity analysis using the RDKit library.

Processes and analyzes multiple physiological signals (ECG, respiration, EDA, EMG, PPG, EOG) together using NeuroKit2, including cross-signal features like RSA and event-related analysis.

Sets up Git-based version control for data science projects, handling notebooks, datasets, and pipelines with DVC and nbstripout.

Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.