jimmc414/kosmos

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pubchem-database Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarit…

jimmc414/kosmos

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pubmed-database Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation manageme…

jimmc414/kosmos

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pufferlib This skill should be used when working with reinforcement learning tasks including high-performance RL training, cust…

jimmc414/kosmos

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pydeseq2 Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR co…

jimmc414/kosmos

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pydicom Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when rea…

jimmc414/kosmos

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pyhealth Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data…

jimmc414/kosmos

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pymatgen Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project i…

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pymc-bayesian-modeling Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, post…

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pyopenms Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflow…

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pysam Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, c…

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rdkit Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerp…

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scanpy Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes…

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scholar-evaluation Systematic framework for evaluating scholarly and research work based on the ScholarEval methodology. This skill shou…

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scientific-brainstorming Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop…

jimmc414/kosmos

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scientific-critical-thinking Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence…

jimmc414/kosmos

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scikit-survival Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skil…

jimmc414/kosmos

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scvi-tools This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, sc…

jimmc414/kosmos

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shap Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining …

jimmc414/kosmos

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simpy Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with…

jimmc414/kosmos

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string-database Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichm…

jimmc414/kosmos

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torch-geometric Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, m…

jimmc414/kosmos

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torchdrug Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasonin…

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umap-learn UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HD…

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uniprot-database Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workf…

jimmc414/kosmos

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vaex Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex…

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zarr-python Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatib…

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zinc-database Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for doc…

jimmc414/kosmos

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fda-database Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identifi…

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fluidsim Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations incl…

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