@K-Dense-AI
K-Dense
- Skills
- 40
- GitHub stars
- 57k
- Installs
- 328k
Top skills by K-Dense
K-Dense
Scientific Agent Skills
K-Densealphagenome
Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq…
K-Dense
Scientific Agent Skills
K-Denseanalytical-method-validation
Plans, executes, and documents validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP //, ICH M10 bioanalytical, CLSI EP, or…
K-Dense
Scientific Agent Skills
K-Densearbor
Applies Arbor Hypothesis Tree Refinement to research artifacts with repeatable evaluators, including model training, agent harnesses, data synthesis and benchmark optimization. Uses…
K-Dense
Scientific Agent Skills
K-Densearboreto
Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for transcription factor-target association ranking…
K-Dense
Scientific Agent Skills
K-Denseautoskill
Analyzes user-requested Screenpipe history windows to detect repeated research workflows, match existing scientific skills, and stage new skill drafts or composition recipes for review…
K-Dense
Scientific Agent Skills
K-Densebids
Organizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets. Supports organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS…
K-Dense
Scientific Agent Skills
K-Densebioservices
Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database protein annotation, pathway retrieval…
K-Dense
Scientific Agent Skills
K-Densebulk-rnaseq
Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantification, biological replication…
K-Dense
Scientific Agent Skills
K-Densecantera
Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use for combustion kinetics, closed…
K-Dense
Scientific Agent Skills
K-Densecellprofiler
Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports image/channel manifests, headless batch…
K-Dense
Scientific Agent Skills
K-Densecitation-management
Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, and generate properly…
K-Dense
Scientific Agent Skills
K-Denseclinical-decision-support
Prepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Supports aggregate or…
K-Dense
Scientific Agent Skills
K-Denseclinical-reports
Creates safety-bounded draft structures and runs local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic…
K-Dense
Scientific Agent Skills
K-Densedeepchem
Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked labels, graph models and explicit…
K-Dense
Scientific Agent Skills
K-Densedeeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
K-Dense
Scientific Agent Skills
K-Densedepmap
Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics biomarkers, and PRISM drug sensitivity. Supports…
K-Dense
Scientific Agent Skills
K-Densediffdock
Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose triage, confidence interpretation, and…
K-Dense
Scientific Agent Skills
K-Densednanexus-integration
Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Supports DNAnexus data transfers, dxapp.json…
K-Dense
Scientific Agent Skills
K-Denseesm
Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to local model inference and Biohub hosted clients, including former…
K-Dense
Scientific Agent Skills
K-Denseetetoolkit
Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O, topology edits and pattern matching…
K-Dense
Scientific Agent Skills
K-Denseexa-search
Searches scientific and technical web content with Exa and extracts page or PDF text from URLs in batches. Supports scholarly discovery with the publication category and academic domain…
K-Dense
Scientific Agent Skills
K-Denseexperimental-design
Designs experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable. Use whenever someone…
K-Dense
Scientific Agent Skills
K-Denseexploratory-data-analysis
Performs bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata…
K-Dense
Scientific Agent Skills
K-Denseadaptyv
Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory progress, and retrieve results. Applies…
K-Dense
Scientific Agent Skills
K-Denseaeon
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use…
K-Dense
Scientific Agent Skills
K-Denseanndata
Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for…
K-Dense
Scientific Agent Skills
K-Denseastropy
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. Use when…
K-Dense
Scientific Agent Skills
K-Densebenchling-integration
Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with…
K-Dense
Scientific Agent Skills
K-Densebiopython
Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Supports batch processing, custom…
K-Dense
Scientific Agent Skills
K-Densecellxgene-census
Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices…
K-Dense
Scientific Agent Skills
K-Densecirq
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware…
K-Dense
Scientific Agent Skills
K-Densecobrapy
Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes, gap filling, and SBML model…
K-Dense
Scientific Agent Skills
K-Denseconsciousness-council
Structures a multi-perspective council exercise for decisions, research trade-offs, and creative challenges. Simulates thinking archetypes, separates evidence from assumptions and values…
K-Dense
Scientific Agent Skills
K-Densedask
Scales pandas, NumPy, and custom Python research workflows beyond memory or across clusters with Dask. Covers DataFrames, Arrays, Bags, Futures, chunking, schedulers, and distributed…
K-Dense
Scientific Agent Skills
K-Densedatabase-lookup
Queries documented public database APIs with explicit endpoints, filters, pagination, and provenance. Used when a scientific, regulatory, financial, or other database-backed fact must be…
K-Dense
Scientific Agent Skills
K-Densedatalad
Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provenance with datalad run, rerun, and containers-run. Use when cloning or…
K-Dense
Scientific Agent Skills
K-Densedatamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints…
K-Dense
Scientific Agent Skills
K-Densedeepspot-m
Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Used for predicted log1p-CPM expression from 224x224 tiles at about 20x, querying the…
K-Dense
Scientific Agent Skills
K-Densedhdna-profiler
Applies the DHDNA framework as an exploratory rubric for reasoning and writing patterns in supplied text. Used for explicit requests for DHDNA, cognitive-style reflection, a…
K-Dense
Scientific Agent Skills
K-Densebgpt-paper-search
Searches BGPT scientific papers by topic or DOI and retrieves claim-level evidence extracted from full text, including experiments, reported statistics, scope, limitations, and provenance…