Skills matching the name, description or GitHub author.
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service o...
Python computations in science and engineering (pycse) - helps with scientific computing tasks including nonlinear regression, uncertainty quantification, design of experiments (DOE), Latin hypercube sampling,...
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS sys...
A skill for analyzing data using Python (pandas) and generating professional visualizations (matplotlib/seaborn).
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures,...
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct...
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
Mass spectrometry toolkit (OpenMS Python). Process mzML/mzXML, peak picking, feature detection, peptide ID, proteomics/metabolomics workflows, for LC-MS/MS analysis.
CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads....
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
Expert guidance for Design of Experiments (DOE) in Python - interactive goal-driven design selection, classical DOE (factorial, response surface, screening), Bayesian optimization with Gaussian processes, model...
Use the M4 Python API to query clinical datasets (MIMIC-IV, eICU) programmatically. Triggers on "M4 API", "query MIMIC with Python", "clinical data analysis", "EHR data", "execute SQL on MIMIC", or when writing...
Research Python/Z3 patterns and APIs for semantic theory development. Invoke for Python-language research tasks.
Computational text analysis for sociology research using R or Python. Guides you through topic models, sentiment analysis, classification, and embeddings with systematic validation. Supports both traditional (L...
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment...
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal pro...
Julia package equivalents for 137 K-Dense-AI scientific skills. Maps Python bioinformatics, chemistry, ML, quantum, and data science packages to native Julia ecosystem.
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices...
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service o...
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment...
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID map...
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
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