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Research & Science · K-Dense-AI/scientific-agent-skills
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 49 | 49.Cellprofiler Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. | K-Dense-AI/ | 48k | 1 repo | ~1.9k | Automated safety check: Pass | MIT | 6 days ago |
| 50 | Reads, validates, and safely exports protocols.io data with current official REST/MCP contracts, or creates non-executing mutation plans. | K-Dense-AI/ | 48k | 1 repo | ~3.4k | Automated safety check: Notes | MIT | 6 days ago |
| 51 | 51.Pyhealth Builds and validates PyHealth clinical machine-learning pipelines for EHR, signals, imaging, and medical codes. | K-Dense-AI/ | 48k | 1 repo | ~2.1k | Automated safety check: Pass | MIT | 6 days ago |
| 52 | 52.Pylabrobot Develops and reviews PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations. | K-Dense-AI/ | 48k | 1 repo | ~3k | Automated safety check: Notes | MIT | 6 days ago |
| 53 | 53.Scanpy Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or… | K-Dense-AI/ | 48k | 1 repo | ~5.1k | Automated safety check: Pass | BSD-3-Clause | 6 days ago |
| 54 | Tracks physical units and propagates measurement uncertainty in scientific calculations using pint and uncertainties. | K-Dense-AI/ | 48k | 1 repo | ~5.4k | Automated safety check: Notes | MIT | 6 days ago |
| 55 | Prepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. | K-Dense-AI/ | 48k | 1 repo | ~3.5k | Automated safety check: Pass | MIT | 6 days ago |
| 56 | Supports research proposal preparation and review for NSF, NIH, DOE, DARPA, and Taiwan NSTC, including opportunity-specific requirements, aims, review criteria, budgets, broader impacts, forms, and… | K-Dense-AI/ | 48k | 1 repo | ~4.3k | Automated safety check: Notes | MIT | 6 days ago |
| 57 | 57.Astropy Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. | K-Dense-AI/ | 48k | 1 repo | ~4.3k | Automated safety check: Pass | BSD-3-Clause | 6 days ago |
| 58 | 58.Arbor Applies Arbor Hypothesis Tree Refinement to research artifacts with repeatable evaluators, including model training, agent harnesses, data synthesis and benchmark optimization. | K-Dense-AI/ | 48k | 1 repo | ~4.3k | Automated safety check: Notes | MIT | 6 days ago |
| 59 | 59.Bids Organizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets. | K-Dense-AI/ | 48k | 1 repo | ~3.7k | Automated safety check: Pass | MIT | 6 days ago |
| 60 | 60.Bioservices Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. | K-Dense-AI/ | 48k | 1 repo | ~3k | Automated safety check: Notes | MIT | 6 days ago |
| 61 | Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. | K-Dense-AI/ | 48k | 1 repo | ~3.4k | Automated safety check: Notes | MIT | 6 days ago |
| 62 | Structures a multi-perspective council exercise for decisions, research trade-offs, and creative challenges. | K-Dense-AI/ | 48k | 1 repo | ~3.5k | Automated safety check: Pass | MIT | 6 days ago |
| 63 | 63.Datalad Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provenance with datalad run, rerun, and containers-run. | K-Dense-AI/ | 48k | 1 repo | ~4.4k | Automated safety check: Notes | MIT | 6 days ago |
| 64 | 64.Deepchem Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked labels, graph models and explicit pretrained… | K-Dense-AI/ | 48k | 1 repo | ~2.2k | Automated safety check: Notes | MIT | 6 days ago |
| 65 | 65.Depmap Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics biomarkers, and PRISM drug sensitivity. | K-Dense-AI/ | 48k | 1 repo | ~3.5k | Automated safety check: Pass | CC-BY-4.0 | 6 days ago |
| 66 | Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. | K-Dense-AI/ | 48k | 1 repo | ~3.1k | Automated safety check: Pass | MIT | 6 days ago |
| 67 | 67.Etetoolkit Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. | K-Dense-AI/ | 48k | 1 repo | ~3.3k | Automated safety check: Notes | GPL-3.0-or-later | 6 days ago |
| 68 | 68.Exa Search Searches scientific and technical web content with Exa and extracts page or PDF text from URLs in batches. | K-Dense-AI/ | 48k | 1 repo | ~1.6k | Automated safety check: Notes | MIT | 6 days ago |
| 69 | 69.Geniml Supports audited local Geniml genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenizer compatibility, and assess consensus universes. | K-Dense-AI/ | 48k | 1 repo | ~4k | Automated safety check: Notes | MIT | 6 days ago |
| 70 | Detects host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before a clearly resource-sensitive local workload. | K-Dense-AI/ | 48k | 1 repo | ~2.9k | Automated safety check: Pass | MIT | 6 days ago |
| 71 | 71.Gget Queries 20+ bioinformatics resources through CLI/Python. An agent skill from K-Dense-AI/scientific-agent-skills. | K-Dense-AI/ | 48k | 1 repo | ~2.8k | Automated safety check: Notes | BSD-2-Clause | 6 days ago |
| 72 | 72.Gtars Supports Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and… | K-Dense-AI/ | 48k | 1 repo | ~3.8k | Automated safety check: Notes | MIT | 6 days ago |
| 73 | Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog. | K-Dense-AI/ | 48k | 1 repo | ~2.9k | Automated safety check: Notes | MIT | 6 days ago |
| 74 | Integrates with the official LabArchives ELN REST-like API and Inventory API v1. | K-Dense-AI/ | 48k | 1 repo | ~2.9k | Automated safety check: Notes | MIT | 6 days ago |
| 75 | 75.Lamindb Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections, branches, storage… | K-Dense-AI/ | 48k | 1 repo | ~2.1k | Automated safety check: Pass | Apache-2.0 | 6 days ago |
| 76 | 76.Medchem Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query… | K-Dense-AI/ | 48k | 1 repo | ~3.9k | Automated safety check: Notes | Apache-2.0 | 6 days ago |
| 77 | 77.Networkx Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. | K-Dense-AI/ | 48k | 1 repo | ~4.2k | Automated safety check: Pass | BSD-3-Clause | 6 days ago |
| 78 | 78.Nextflow Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows. | K-Dense-AI/ | 48k | 1 repo | ~3.7k | Automated safety check: Pass | Apache-2.0 | 6 days ago |
| 79 | 79.Paperclip Searches and reads biomedical papers, FDA/PMDA/EMA documents, clinical trials, and protein records with the GXL Paperclip CLI and Python SDK. | K-Dense-AI/ | 48k | 1 repo | ~3.2k | Automated safety check: Notes | MIT | 6 days ago |
| 80 | 80.Pennylane Builds and differentiates PennyLane quantum circuits, hybrid PyTorch or JAX models, molecular VQE and QAOA workflows. | K-Dense-AI/ | 48k | 1 repo | ~1.8k | Automated safety check: Notes | Apache-2.0 | 6 days ago |
| 81 | Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. | K-Dense-AI/ | 48k | 1 repo | ~2.3k | Automated safety check: Pass | MIT | 6 days ago |
| 82 | 82.Polars Bio Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and FASTQ data. | K-Dense-AI/ | 48k | 1 repo | ~3.2k | Automated safety check: Notes | Apache-2.0 | 6 days ago |
| 83 | 83.Pydicom Reads, inspects, writes, transforms, and preflights local DICOM datasets and pixel data. | K-Dense-AI/ | 48k | 1 repo | ~4.8k | Automated safety check: Pass | MIT | 6 days ago |
| 84 | 84.Pymoo Solves and validates single-, multi-, and many-objective optimization with pymoo, including NSGA-II, NSGA-III, MOEA/D, constraints, Pareto approximations, reference directions, and ZDT/DTLZ… | K-Dense-AI/ | 48k | 1 repo | ~3.5k | Automated safety check: Notes | Apache-2.0 | 6 days ago |
| 85 | 85.Pyopenms Processes mass spectrometry data with pyOpenMS. An agent skill from K-Dense-AI/scientific-agent-skills. | K-Dense-AI/ | 48k | 1 repo | ~3.1k | Automated safety check: Notes | BSD-3-Clause | 6 days ago |
| 86 | 86.Pysam Provides Python/HTSlib workflows for genomic files. An agent skill from K-Dense-AI/scientific-agent-skills. | K-Dense-AI/ | 48k | 1 repo | ~3.4k | Automated safety check: Notes | MIT | 6 days ago |
| 87 | Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. | K-Dense-AI/ | 48k | 1 repo | ~2.2k | Automated safety check: Pass | MIT | 6 days ago |
| 88 | 88.Relion Validates and executes RELION single-particle cryo-EM refinement and half-map postprocessing. | K-Dense-AI/ | 48k | 1 repo | ~2k | Automated safety check: Pass | MIT | 6 days ago |
| 89 | 89.Scvi Tools Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression. | K-Dense-AI/ | 48k | 1 repo | ~2.6k | Automated safety check: Pass | BSD-3-Clause | 6 days ago |
| 90 | Calculates sample sizes and statistical power for study planning. | K-Dense-AI/ | 48k | 1 repo | ~4.4k | Automated safety check: Notes | MIT | 6 days ago |
| 91 | 91.Sympy Performs exact symbolic mathematics with SymPy for algebra, calculus, equation solving, symbolic linear algebra, physics, and lambdify or LaTeX code generation. | K-Dense-AI/ | 48k | 1 repo | ~3.3k | Automated safety check: Notes | MIT | 6 days ago |
| 92 | 92.Tamarind Provides access to a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. | K-Dense-AI/ | 48k | 1 repo | ~3.4k | Automated safety check: Pass | MIT | 6 days ago |
| 93 | 93.Tiledbvcf Stores and retrieves genomic variant calls with TileDB-VCF. An agent skill from K-Dense-AI/scientific-agent-skills. | K-Dense-AI/ | 48k | 1 repo | ~3.5k | Automated safety check: Pass | MIT | 6 days ago |
| 94 | 94.Torchdrug Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein representation learning, and… | K-Dense-AI/ | 48k | 1 repo | ~3k | Automated safety check: Notes | Apache-2.0 | 6 days ago |
| 95 | Supports structured what-if scenario analysis for research planning, experimental contingencies, and scientific project decisions. | K-Dense-AI/ | 48k | 1 repo | ~2.9k | Automated safety check: Pass | CC-BY-NC-4.0 | 6 days ago |
| 96 | Generates scientific diagram drafts using Nano Banana 2 AI with smart iterative refinement. | K-Dense-AI/ | 48k | 1 repo | ~5.1k | Automated safety check: Notes | MIT | 6 days ago |
