k-dense-ai: skills, plugins and MCP servers

scanpy K-Dense-AI skill A skill with ready-made CLI scripts for the full single-cell RNA-seq workflow: QC, normalization, clustering, marker genes, visualization. Use it when you want Scanpy results without writing the pipeline by hand. Claude Code CX Codex Cursor +1 1,900installs rdkit K-Dense-AI skill Guides coding agents through cheminformatics tasks in Python, including SMILES parsing, descriptor calculations, and 3D coordinate generation. Claude Code CX Codex Cursor +1 1,900installs modal K-Dense-AI skill Guides Python workloads on Modal, from web endpoints to GPU model training. Use it when deploying cloud jobs through the Modal SDK. Claude Code CX Codex Cursor +1 1,900installs gget K-Dense-AI skill Bioinformatics skill providing unified access to over 20 genomic databases via CLI and Python. Useful for gene lookups, alignments, and protein structure downloads. Claude Code CX Codex Cursor +1 1,900installs clinical-reports K-Dense-AI skill Builds draft skeletons for clinical reports and checks them with local scripts. Inputs must be synthetic, de-identified, or aggregate data. Claude Code CX Codex Cursor +1 1,900installs anndata K-Dense-AI skill Skill to create, read, and transform annotated data matrices in h5ad and Zarr formats. Integrates with the scverse ecosystem for transcriptomics and other metadata-rich data analysis. Claude Code CX Codex Cursor +1 1,900installs bioservices K-Dense-AI skill Guides Python workflows using BioServices to query biological databases. Useful for mapping protein IDs, extracting KEGG pathways, and resolving chemical identifiers. Claude Code CX Codex Cursor +1 1,900installs hypogenic K-Dense-AI skill Skill to plan and audit HypoGeniC, a tool that generates candidate textual hypotheses from labeled datasets using LLM. Use it if you work with the hypogenic package, its task configs, or HypoBench datasets. Claude Code CX Codex Cursor +1 1,900installs simpy K-Dense-AI skill Builds, tests, and inspects process-based discrete-event simulations using SimPy. Helpful for modeling service queues, logistics, and resource contention. Claude Code CX Codex Cursor +1 1,900installs geomaster K-Dense-AI skill Guides geospatial research work with satellite imagery, vector and raster GIS data, coordinate systems, spatial statistics, and Earth observation models. Claude Code CX Codex Cursor +1 1,900installs scikit-bio K-Dense-AI skill Analyzes biological sequences, alignments, and phylogenetic trees directly in your terminal. Helpful for microbiome workflows and ecology data. Claude Code CX Codex Cursor +1 1,900installs consciousness-council K-Dense-AI skill Runs a council of thinking archetypes over a hard choice, keeps facts apart from assumptions and values, and returns a conditional recommendation. Claude Code CX Codex Cursor +1 1,900installs stable-baselines3 K-Dense-AI skill A skill for training reinforcement learning agents with Stable Baselines3. Supports PPO, SAC, DQN and other algorithms, works with Gymnasium custom environments and vectorized rollouts. Claude Code CX Codex Cursor +1 1,900installs geopandas K-Dense-AI skill Guides Python geospatial workflows using GeoPandas, audits vector geometries, and verifies CRS transformations before execution. Claude Code CX Codex Cursor +1 1,900installs research-lookup K-Dense-AI skill Collects verified academic articles and references for a manuscript or review when you need 60+ sources. Uses parallel search, extracts data from PDFs and web sources, supports deep exhaustive search and optional Perplexity. Claude Code CX Codex Cursor +1 1,900installs biopython K-Dense-AI skill Automates computational biology workflows: parses sequence files, runs alignments, and fetches records via NCBI Entrez. Claude Code CX Codex Cursor +1 1,900installs torch-geometric K-Dense-AI skill Guides work with PyTorch Geometric graph neural networks, from graph data setup to classification tasks. Use it when a project relies on torch_geometric. Claude Code CX Codex Cursor +1 1,900installs venue-templates K-Dense-AI skill Prepares journal manuscripts, conference papers, research posters, and grant documents with current venue rules and bundled LaTeX scaffolds. Verifies page limits, anonymity requirements, and formatting before submission. Claude Code CX Codex Cursor +1 1,900installs open-notebook K-Dense-AI skill Organizes research notes, citations, and document chat using self-hosted storage and AI providers. Helpful for managing an Open Notebook setup directly from your agent. Claude Code CX Codex Cursor +1 1,900installs scikit-survival K-Dense-AI skill A skill that walks an agent through scikit-survival 0.28.0: building, tuning and auditing survival models on censored data, with metrics that account for censoring. Claude Code CX Codex Cursor +1 1,900installs hugging-science K-Dense-AI skill A skill to find and evaluate scientific datasets, models, and interactive demos via the Hugging Science catalog. Use it when you need an ML resource for biology, chemistry, genomics, materials science, climate, or physics. Claude Code CX Codex Cursor +1 1,800installs ginkgo-cloud-lab K-Dense-AI skill Assists with protocol selection, input files, pricing checks, and orders for Ginkgo Bioworks Cloud Lab. Useful for RNA synthesis and automated protein expression. Claude Code CX Codex Cursor +1 1,800installs primekg K-Dense-AI skill Wraps the PrimeKG precision-medicine CSV in pandas helpers, so the agent can look up typed nodes, neighbours, disease summaries and short paths without leaving the repo. Claude Code CX Codex Cursor +1 1,800installs exa-search K-Dense-AI skill Skill for searching scientific and technical content via Exa with text extraction from pages and PDFs in batches. Supports filtering by publication category and academic domains. Claude Code CX Codex Cursor +1 1,700installs autoskill K-Dense-AI skill Analyzes Screenpipe activity windows to detect repeating research workflows and drafts new skills for review. Runs strictly on explicit user demand. Claude Code CX Codex Cursor +1 1,700installs nextflow K-Dense-AI skill Guides your AI agent in writing, running, and debugging Nextflow DSL2 pipelines and nf-core workflows on HPC or cloud runners. Claude Code CX Codex Cursor +1 1,400installs pathway-enrichment K-Dense-AI skill Runs pathway and gene-set enrichment analysis on gene lists or ranked data, finds over-represented GO terms, KEGG, Reactome, MSigDB. Needed after differential expression, CRISPR screens, or clustering. Claude Code CX Codex Cursor +1 1,400installs bulk-rnaseq K-Dense-AI skill Prepares bulk RNA-seq reads, Salmon, and STAR outputs into validated gene-level count matrices for differential expression in PyDESeq2. Claude Code CX Codex Cursor +1 1,400installs pacsomatic K-Dense-AI skill Prepares a matched tumor-normal run of nf-core/pacsomatic on PacBio HiFi data: builds the samplesheet, writes launch artifacts, submits the Nextflow driver to a scheduler. Claude Code CX Codex Cursor +1 1,400installs statistical-power K-Dense-AI skill Calculates how many observations your study needs to reliably detect a meaningful effect. Supports protocol planning, grant submissions, and pre-registration — from basic t-tests to complex mixed models and survival analysis. Claude Code CX Codex Cursor +1 1,300installs arbor K-Dense-AI skill Runs an autonomous optimization loop using hypothesis trees for models, code, and harnesses. Useful when organizing dozens of experimental trials without losing past findings. Claude Code CX Codex Cursor +1 1,200installs pi-agent K-Dense-AI skill Helps you install and configure Pi, then build extensions, integrations, and terminal UI components around it. Claude Code CX Codex Cursor +1 1,200installs onekgpd K-Dense-AI skill Queries the 1000 Genomes Project cohort at the participant level. It identifies variant carriers across 3,202 individuals and calculates relatedness. Claude Code CX Codex Cursor +1 1,100installs tamarind K-Dense-AI skill Runs Tamarind Bio structural biology and molecular design tools through its REST API or MCP server. Use it for cloud jobs without local GPUs. Claude Code CX Codex Cursor +1 1,100installs genomic-coordinates K-Dense-AI skill Converts genomic coordinates between BED, VCF, and GTF formats, and normalises variant representations. Useful when reconciling coordinate systems, indels, and assembly contigs. Claude Code CX Codex Cursor +1 939installs ontology-term-resolution K-Dense-AI skill Resolves free-text scientific labels to ontology term IDs and validates CURIEs via EBI OLS4. Useful for preparing dataset metadata for GEO, BioSamples, or CELLxGENE. Claude Code CX Codex Cursor +1 937installs pkpd-modeling K-Dense-AI skill Runs non-compartmental and compartmental PK/PD calculations on concentration-time data, then spells out what the numbers assume. Claude Code CX Codex Cursor +1 924installs deepspot-m K-Dense-AI skill Reads a 224x224 H&E tile and returns predicted log1p-CPM expression for the genes you ask about. Useful when you want spatial transcriptomics from a slide you have already scanned. Claude Code CX Codex Cursor +1 866installs relsa-severity-assessment K-Dense-AI skill Calculates multivariate RELSA severity scores and ARIMA-based score forecasts for animal studies. Useful for 3Rs reporting and EU Directive 2010/63/EU compliance. Claude Code CX Codex Cursor +1 863installs ncats-arax K-Dense-AI skill Skill for querying the NCATS Translator ARAX knowledge graph: typed edges with provenance, entity normalization, and offline review of saved TRAPI responses. Claude Code CX Codex Cursor +1 858installs