1,133 skills found · Page 31 of 38
Microck / biorxiv-databaseEfficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
Microck / cobrapyConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
Microck / data-transformTransform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
Microck / bioservicesPrimary 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 REST control, use individual database skills (uniprot-database, kegg-database).
Microck / cirqQuantum computing framework for building, simulating, optimizing, and executing quantum circuits. Use this skill when working with quantum algorithms, quantum circuit design, quantum simulation (noiseless or noisy), running on quantum hardware (Google, IonQ, AQT, Pasqal), circuit optimization and co…
Microck / data-export-pdfCreate professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
Microck / backend-ai-guideExpert guide for Backend.AI distributed computing platform. Automatically activates when users ask about: - Backend.AI architecture, components (Manager, Agent, Storage Proxy, Webserver, App Proxy) - Features (session scheduling, Sokovan orchestrator, multi-tenancy, resource allocation) - APIs (REST…
hypnguyen1209 / coding-masteryUse when writing security tooling, exploits, scanners, or C2 in Python/C/Go/Rust/ASM — systems & network programming, automation, cryptography implementation
hypnguyen1209 / ai-agent-redteamUse when red-teaming an agentic AI / LLM application — indirect & zero-click prompt injection, MCP tool poisoning, persistent memory poisoning, excessive-agency tool abuse, multi-turn jailbreaks, PyRIT/Garak/Promptfoo harnesses
giuseppe-trisciuoglio / developer-kitModular plugin marketplace for Claude Code and agentic CLIs, with validated, spec-driven skills, agents, commands, and workflows for Java, TypeScript, Python, PHP, AWS, and AI.
jaechang-hits / opentrons-integrationOpentrons Protocol API v2 for OT-2/Flex: Python protocols for pipetting, serial dilutions, PCR, plate replication; control thermocycler, heater-shaker, magnetic, temperature modules. Use pylabrobot for multi-vendor.
jaechang-hits / plotly-interactive-visualizationInteractive visualization with Plotly. 40+ chart types (scatter, line, heatmap, 3D, geographic) with hover, zoom, pan. Two APIs: Plotly Express (DataFrame) and Graph Objects (fine control). For static publication figures use matplotlib; for statistical grammar use seaborn.
jaechang-hits / seaborn-statistical-visualizationStatistical visualization on matplotlib + pandas. Distributions (histplot, kdeplot, violin, box), relational (scatter, line), categorical, regression, correlation heatmaps. Auto aggregation/CIs. Use plotly for interactive; matplotlib for low-level.
jaechang-hits / pymc-bayesian-modelingBayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison, prediction. Hierarchical, logistic, GP variants; predictive checks.
jaechang-hits / scikit-survival-analysisTime-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored data. C-index, Brier, time-dependent AUC; Kaplan-Meier, Nelson-Aalen, competing risks. Pipeline/GridSearchCV compatible.
jaechang-hits / statsmodels-statistical-modelingPython statistical modeling: regression (OLS, WLS, GLM), discrete (Logit, Poisson, NegBin), time series (ARIMA, SARIMAX, VAR), with rigorous inference, diagnostics, and hypothesis tests. Use scikit-learn for ML; statistical-analysis for test choice.
jaechang-hits / flowio-flow-cytometryParse/write FCS (Flow Cytometry) files v2.0-3.1. Events as NumPy, channel metadata, multi-dataset files, CSV/FCS export. Use FlowKit for gating/compensation.
jaechang-hits / napari-image-viewerInteractive viewer for microscopy. Displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, Tracks layers; supports annotation, plugin analysis, headless screenshots. Core visualization for Python bioimage workflows.
jaechang-hits / opencv-bioimage-analysisComputer vision for bio-image preprocessing, feature detection, real-time microscopy. Color conversion, morphology, contour/blob detection, template matching, optical flow on fluorescence/brightfield. 10-100× faster than pure Python via C++.
jaechang-hits / pyimagej-fiji-bridgePython bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops. Automates Fiji headlessly from Python. Use scikit-image for pure Python without Fiji plugins; napari for visualization.
jaechang-hits / scikit-image-processingPython image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG), segment (thresholding, watershed, active contours), measure region properties, detect features. SciPy/NumPy ecosystem.
jaechang-hits / trackpy-particle-trackingPython library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. Locate particles (fluorescent spots, colloids, vesicles, cells) per frame, link into trajectories, filter short tracks, and compute MSD for diffusion analysis.
jaechang-hits / matplotlib-scientific-plottingLow-level Python plotting for scientific figures: publication-quality line, scatter, bar, heatmap, contour, 3D; multi-panel layouts; fine control of every element. PNG/PDF/SVG export. Use seaborn for quick stats, plotly for interactive.
jaechang-hits / plotly-interactive-plotsInteractive scientific visualization with Plotly. Two APIs: plotly.express (px) for one-liner DataFrame plots, plotly.graph_objects (go) for trace-level control. 40+ chart types with hover, zoom, pan, animation. Exports HTML or static PNG/SVG/PDF via kaleido.
jaechang-hits / seaborn-statistical-plotsStatistical visualization on matplotlib with native pandas support. Auto aggregation, CIs, grouping for distributions (histplot, kdeplot), categorical (boxplot, violinplot), relational (scatterplot, lineplot), regression (regplot, lmplot), matrix (heatmap, clustermap), grids (pairplot, FacetGrid).
jaechang-hits / biopython-molecular-biologyMolecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries.
jaechang-hits / biopython-sequence-analysisBiopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic trees (Phylo). Use for gene family studies, phylogenomics, comparative genomics, NCBI pipelines.
jaechang-hits / etetoolkitETE Toolkit (ETE3): Python phylogenetic tree analysis and visualization. Parse Newick/NHX/PhyloXML, traverse/annotate nodes, render figures with TreeStyle/NodeStyle, integrate NCBI taxonomy, run PhyloTree comparative genomics. Use for species trees, gene family evolution, annotated tree figures.
jaechang-hits / scikit-bioPython library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees (NJ, UPGMA), diversity (Shannon, Faith PD, Bray-Curtis, UniFrac), ordination (PCoA, CCA, RDA), stats (PERMANOVA, ANOSIM, Mantel), file I/O (FASTA, FASTQ, Newick, BIOM).
jaechang-hits / benchling-integrationBenchling R&D Python SDK: CRUD on registry entities (DNA, RNA, proteins, custom), inventory, ELN, workflow automation. Needs Benchling account and API key. Use biopython for local sequence analysis; pubchem for chemical DBs.
