Skills from K-Dense’s repositories that passed our trust, licence and security gates. Each keeps its author’s attribution.
| Repository | Tier | Verdict | Authorship | Checked | Skills |
|---|---|---|---|---|---|
| K-Dense-AI/claude-scientific-writer | Project | Approved · created 2025-10-27, pushed 2026-11-07, 2559 stars | Written in-house | 2026-11-07 | 26 |
| K-Dense-AI/scientific-agent-skills | Project | Approved · created 2025-10-19, pushed 2026-11-02, 56393 stars | Written in-house | 2026-11-07 | 177 |
Files are mirrored only where the licence allows redistribution; otherwise we link to the source.
K-Dense· Community
A workflow for analyzing pooled CRISPR screens using MAGeCK to identify gene hits and perform quality control.
K-Dense· Community
Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phylogenies.
K-Dense· Community
Provides planning, auditing, and configuration tools for the HypoGeniC package to assist in LLM-based hypothesis generation from labeled text datasets.
K-Dense· Community
A reproducible workflow for processing 1D NMR free-induction decays into phased spectra and integrated regions.
K-Dense· Community
Provides workflows for accessing and evaluating therapeutic machine learning datasets and benchmarks via PyTDC.
K-Dense· Community
A comprehensive framework for geospatial research, covering remote sensing, GIS, spatial statistics, and Earth observation data processing.
K-Dense· Community
A Pythonic wrapper for RDKit simplifying molecular cheminformatics tasks like standardization, fingerprinting, and 3D conformer generation.
K-Dense· Community
Provides Rust, Python, and CLI interfaces for genomic interval processing, set algebra, and signal track generation.
K-Dense· Community
Manage biological datasets, metadata, and lineage using LaminDB for reproducible research.
K-Dense· Community
A structured framework for autonomous research optimization using Hypothesis Tree Refinement to manage experiments and accumulate insights.
K-Dense· Community
Integrate Hugging Face Transformers for model loading, inference, and fine-tuning across NLP, vision, and audio tasks.
K-Dense· Community
A Python client for programmatically managing Zotero reference libraries, collections, and attachments via Web and local APIs.
K-Dense· Community
Parametric CAD for laboratory hardware with automated interface verification and fabrication artifact generation.
K-Dense· Community
Generate and edit images using various AI models via the OpenRouter API.
K-Dense· Community
Generate academic research posters using LaTeX templates and automated preflight tools.
K-Dense· Community
Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue docking, protein-ligand cofolding, MSA generation, molecular dynamics, permeability, descriptor workflows, and related small-molecule or protein modeling tasks. Ideal for programmatic batch screening, multi-step chemistry pipelines, and workflows that would otherwise require maintaining local HPC/GPU infrastructure.
K-Dense· Community
A PyTorch-based library for training and evaluating reinforcement learning agents using standardized algorithms and environments.
K-Dense· Community
A workflow for calculating seawater carbonate chemistry, mineral saturation, and uncertainty propagation using PyCO2SYS.
K-Dense· Community
Query the NCATS ARAX biomedical knowledge graph API for bounded, provenance-rich relationship lookups.
K-Dense· Community
A local-only workflow for preparing structured, evidence-based peer review drafts for scientific manuscripts.
K-Dense· Community
Analyzes and engineers protein glycosylation by scanning canonical N-glycosylation sequons, describing S/T-rich regions, checking curated glycan evidence, and preparing NetNGlyc, NetOGlyc and GlycoSHIELD workflows. Use for glycoprotein engineering, antibody Fc glycosylation, glycan shielding, and site-specific glycoproteomics interpretation.
K-Dense· Community
Parallel and distributed computing library for scaling Python research workflows.
K-Dense· Community
Automates reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counting, and fluorescence measurement.
K-Dense· Community
Integrate with the self-hosted Open Notebook platform to automate research ingestion, context-aware chat, and AI-driven analysis.