k-dense-ai/scientific-agent-skills

v2.72.0MIT

Ready-to-use scientific and research Agent Skills for biology, chemistry, medicine, and related workflows.

GitHub Open Website

allowed-tools

Read98 skills
Bash95 skills
Write92 skills
Edit79 skills
Glob18 skills
Python9 skills
Grep8 skills
Agent1 skill
2 more
- WebFetch1 skill
- WebSearch1 skill

scripts

13c-metabolic-flux
scripts/_mfa_fit.py
scripts/_mfa_model.py
scripts/mfa.py
alphagenome
scripts/_common.py
scripts/atlas_link.py
scripts/atlas_query.py
scripts/score_variants.py
analytical-method-validation
648 more
- scripts/_catalog.py
- scripts/_common.py
- scripts/check_accuracy_precision.py
- scripts/check_bioanalytical_run.py
- scripts/check_detection_limits.py
- scripts/check_response.py
- scripts/compare_methods.py
- scripts/plan_validation.py
- arbor
- scripts/tree.py
- arboreto
- scripts/basic_grn_inference.py
- autoskill
- scripts/autoskill.py
- scripts/backends.py
- scripts/cluster.py
- scripts/doctor.py
- scripts/fetch_window.py
- scripts/match_skills.py
- scripts/promote.py
- scripts/redact.py
- scripts/run.py
- scripts/synthesize.py
- bids
- scripts/update_schema.py
- bioservices
- scripts/batch_id_converter.py
- scripts/compound_cross_reference.py
- scripts/pathway_analysis.py
- scripts/protein_analysis_workflow.py
- bulk-rnaseq
- scripts/_tabular.py
- scripts/build_counts_matrix.py
- scripts/validate_samplesheet.py
- cantera
- scripts/ignition_delay.py
- cellprofiler
- scripts/nuclei_assay.py
- citation-management
- scripts/_common.py
- scripts/doi_to_bibtex.py
- scripts/extract_metadata.py
- scripts/format_bibtex.py
- scripts/search_google_scholar.py
- scripts/search_openalex.py
- scripts/search_pubmed.py
- scripts/validate_citations.py
- clinical-decision-support
- scripts/_common.py
- scripts/cohort_table_generator.py
- scripts/decision_logic_traceability.py
- scripts/deidentification_checklist.py
- scripts/evidence_profile_check.py
- scripts/model_biomarker_evaluation.py
- scripts/survival_plan_validator.py
- scripts/validate_cds_artifact.py
- clinical-reports
- scripts/_common.py
- scripts/check_deidentification.py
- scripts/consistency_checker.py
- scripts/format_adverse_events.py
- scripts/generate_report_template.py
- scripts/provenance_validator.py
- scripts/terminology_validator.py
- scripts/validate_case_report.py
- scripts/validate_trial_report.py
- deepchem
- scripts/_common.py
- scripts/graph_neural_network.py
- scripts/predict_solubility.py
- scripts/transfer_learning.py
- deeptools
- scripts/validate_files.py
- scripts/workflow_generator.py
- depmap
- scripts/depmap_data.py
- diffdock
- scripts/analyze_results.py
- scripts/prepare_batch_csv.py
- scripts/setup_check.py
- dnanexus-integration
- scripts/inspect_dxpy.py
- scripts/validate_dxapp.py
- esm
- scripts/esm_embeddings.py
- etetoolkit
- scripts/quick_visualize.py
- scripts/tree_operations.py
- exa-search
- scripts/exa_extract.py
- scripts/exa_search.py
- experimental-design
- scripts/doe_designs.py
- scripts/randomization.py
- exploratory-data-analysis
- scripts/__init__.py
- scripts/_capabilities.py
- scripts/_common.py
- scripts/_structured.py
- scripts/_tabular.py
- scripts/capability_manifest.py
- scripts/distribution_sensitivity.py
- scripts/eda_analyzer.py
- scripts/image_inspector.py
- scripts/missingness_leakage_audit.py
- scripts/report_scaffold.py
- scripts/sequence_inspector.py
- scripts/tabular_profile.py
- fictiv
- scripts/check_cad_file.py
- scripts/list_dropdown_options.js
- scripts/quote_state.js
- flowio
- scripts/inspect_fcs.py
- flowkit
- scripts/analyze_gates.py
- fluidsim
- scripts/__init__.py
- scripts/_common.py
- scripts/_profiles.py
- scripts/_schema.py
- scripts/budget_summary.py
- scripts/grid_resource_estimator.py
- scripts/output_inventory.py
- scripts/restart_compatibility.py
- scripts/simulation_dry_run.py
- scripts/solver_config_validator.py
- generate-image
- scripts/generate_image.py
- geniml
- scripts/__init__.py
- scripts/_common.py
- scripts/bed_validator.py
- scripts/consensus_plan.py
- scripts/corpus_auditor.py
- scripts/embedding_plan.py
- scripts/model_artifact_inspector.py
- scripts/tokenizer_compatibility.py
- genomic-coordinates
- scripts/_common.py
- scripts/audit_intervals.py
- scripts/check_contigs.py
- scripts/convert_coords.py
- scripts/normalize_variant.py
- geomaster
- scripts/raster_workflows.py
- geopandas
- scripts/_common.py
- scripts/crs_reprojection_plan.py
- scripts/export_plan.py
- scripts/geometry_validity_report.py
- scripts/sensitive_coordinates_checklist.py
- scripts/spatial_join_audit.py
- scripts/vector_inventory.py
- get-available-resources
- scripts/_common.py
- scripts/accelerator_diagnostics.py
- scripts/detect_resources.py
- scripts/plan_workload.py
- scripts/snapshot_tools.py
- gget
- scripts/batch_sequence_analysis.py
- scripts/enrichment_pipeline.py
- scripts/gene_analysis.py
- glycoengineering
- scripts/glycoengineering_tools.py
- scripts/glytoucan_lookup.py
- gtars
- scripts/__init__.py
- scripts/_common.py
- scripts/artifact_inspector.py
- scripts/bed_validator.py
- scripts/coverage_preflight.py
- scripts/execution_plan.py
- scripts/refget_digest_plan.py
- scripts/tokenizer_manifest.py
- hugging-science
- scripts/fetch_catalog.py
- hypogenic
- scripts/__init__.py
- scripts/_common.py
- scripts/audit_dataset.py
- scripts/evaluate_local.py
- scripts/inspect_outputs.py
- scripts/plan_run.py
- scripts/validate_config.py
- hypothesis-generation
- scripts/_common.py
- scripts/audit_evidence_ledger.py
- scripts/check_falsification_controls.py
- scripts/check_operationalization.py
- scripts/generate_preregistration_scaffold.py
- scripts/lint_causal_claims.py
- scripts/validate_hypothesis_schema.py
- scripts/validate_prediction_matrix.py
- imaging-data-commons
- scripts/check_version.py
- infographics
- scripts/generate_infographic.py
- scripts/generate_infographic_ai.py
- iso-standards-readiness
- scripts/_catalog.py
- scripts/_common.py
- scripts/audit_document_records.py
- scripts/check_capa.py
- scripts/check_qmsr_transition.py
- scripts/check_supplier_controls.py
- scripts/check_traceability.py
- scripts/gap_analyzer.py
- scripts/validate_evidence_manifest.py
- scripts/validate_scope_intake.py
- lab-hardware-cad
- scripts/_common.py
- scripts/check.py
- scripts/gen.py
- scripts/snapshot.py
- labarchive-integration
- scripts/entry_operations.py
- scripts/notebook_operations.py
- scripts/setup_config.py
- latchbio-integration
- scripts/inspect_latch_sdk.py
- latex-posters
- scripts/generate_schematic.py
- scripts/generate_schematic_ai.py
- scripts/review_poster.sh
- liteparse
- scripts/batch_parse_dir.py
- literature-review
- scripts/generate_pdf.py
- scripts/generate_schematic.py
- scripts/generate_schematic_ai.py
- scripts/search_databases.py
- scripts/verify_citations.py
- mageck
- scripts/screen_analysis.py
- marine-carbonate-chemistry
- scripts/solve_carbonate.py
- market-research-reports
- scripts/_common.py
- scripts/audit_claim_citations.py
- scripts/calculate_market_sizing.py
- scripts/check_unit_consistency.py
- scripts/forecast_sensitivity.py
- scripts/generate_report_scaffold.py
- scripts/validate_competitor_matrix.py
- scripts/validate_evidence_ledger.py
- markitdown
- scripts/batch_convert.py
- scripts/convert_literature.py
- scripts/inspect_installation.py
- matchms
- scripts/library_search.py
- matlab
- scripts/_common.py
- scripts/generate_function_scaffold.py
- scripts/inventory_mat_file.py
- scripts/plan_batch_command.py
- scripts/plan_python_compatibility.py
- scripts/reproducibility_report.py
- scripts/scan_m_code.py
- scripts/validate_project_manifest.py
- matplotlib
- scripts/plot_template.py
- scripts/style_configurator.py
- medchem
- scripts/filter_molecules.py
- ncats-arax
- scripts/arax_client.py
- neurokit2
- scripts/_common.py
- scripts/ecg_hrv_pipeline.py
- scripts/eda_pipeline.py
- scripts/generate_synthetic.py
- scripts/inspect_signal.py
- scripts/plan_epochs.py
- scripts/validate_multimodal.py
- neuropixels-analysis
- assets/analysis_template.py
- scripts/_common.py
- scripts/compute_metrics.py
- scripts/explore_recording.py
- scripts/export_to_phy.py
- scripts/neuropixels_pipeline.py
- scripts/preprocess_recording.py
- scripts/run_sorting.py
- nmrglue
- scripts/process_1d.py
- nwb-conversion
- scripts/convert_session.py
- omero-integration
- scripts/export_image_metadata.py
- scripts/inventory.py
- scripts/omero_common.py
- scripts/plan_transfer.py
- scripts/validate_config.py
- onekgpd
- scripts/onekgpd_api.py
- scripts/onekgpd_meta.py
- ontology-term-resolution
- scripts/id_client.py
- scripts/lookup_prefix.py
- scripts/map_terms.py
- scripts/ols_client.py
- scripts/resolve_terms.py
- scripts/validate_terms.py
- scripts/zooma_client.py
- open-notebook
- scripts/_common.py
- scripts/chat_interaction.py
- scripts/notebook_management.py
- scripts/source_ingestion.py
- openpiv
- scripts/__init__.py
- scripts/analyze.py
- scripts/run_example.py
- scripts/runner.py
- opentrons-integration
- scripts/absorbance_reader_template.py
- scripts/basic_protocol_template.py
- scripts/ot2_basic_protocol_template.py
- scripts/pcr_setup_template.py
- scripts/runtime_parameters_template.py
- scripts/serial_dilution_template.py
- pacsomatic
- scripts/run_pacsomatic.py
- paper-lookup
- scripts/_common.py
- scripts/arxiv_atom.py
- scripts/jats_to_text.py
- scripts/openalex_abstract.py
- scripts/paginate.py
- pathml
- scripts/_common.py
- scripts/image_qc.py
- scripts/plan_inference.py
- scripts/plan_pipeline.py
- scripts/slide_manifest.py
- scripts/validate_spatial_schema.py
- pathogen-variant-surveillance
- scripts/lapis_client.py
- scripts/lineage_prevalence.py
- scripts/mutation_profile.py
- scripts/reporting_lag.py
- scripts/resolve_lineage.py
- pathway-enrichment
- scripts/run_enrichment.py
- peer-review
- scripts/_common.py
- scripts/audit_citations.py
- scripts/audit_statistics_reproducibility.py
- scripts/generate_review_scaffold.py
- scripts/lint_review.py
- scripts/select_reporting_guidelines.py
- scripts/validate_claim_evidence.py
- scripts/validate_review_intake.py
- phylogenetics
- scripts/phylogenetic_analysis.py
- pkpd-modeling
- scripts/_common.py
- scripts/_models.py
- scripts/allometry_and_fih.py
- scripts/bioequivalence.py
- scripts/check_popk_dataset.py
- scripts/ddi_static.py
- scripts/exposure_response.py
- scripts/fit_compartmental.py
- scripts/nca.py
- scripts/simulate_regimen.py
- scripts/tdm_bayes.py
- pptx-posters
- scripts/_common.py
- scripts/_manifest.py
- scripts/_pptx.py
- scripts/check_layout.py
- scripts/check_palette.py
- scripts/generate_poster.py
- scripts/inspect_pptx.py
- scripts/inventory_images.py
- scripts/plan_export.py
- scripts/validate_manifest.py
- primekg
- scripts/query_primekg.py
- primer-design
- scripts/_common.py
- scripts/_specificity.py
- scripts/check_thermodynamics.py
- scripts/design_primers.py
- scripts/screen_specificity.py
- protocolsio-integration
- scripts/__init__.py
- scripts/_common.py
- scripts/pagination_helper.py
- scripts/plan_write_request.py
- scripts/protocols_read.py
- scripts/validate_auth_config.py
- scripts/validate_protocol_json.py
- pufferlib
- scripts/__init__.py
- scripts/_common.py
- scripts/benchmark_vectorization.py
- scripts/env_contract_validator.py
- scripts/env_template.py
- scripts/inspect_checkpoint.py
- scripts/repro_plan.py
- scripts/train_template.py
- scripts/validate_plan.py
- pybamm
- scripts/simulate_battery.py
- pycalphad
- scripts/equilibrate.py
- pydeseq2
- scripts/run_deseq2_analysis.py
- pydicom
- scripts/__init__.py
- scripts/_common.py
- scripts/anonymize_dicom.py
- scripts/deidentification_audit.py
- scripts/dicom_inventory.py
- scripts/dicom_to_image.py
- scripts/extract_metadata.py
- scripts/pixel_frame_planner.py
- scripts/transfer_syntax_inspector.py
- scripts/uid_mapping_validator.py
- pyhealth
- assets/starter_pipeline.py
- pylabrobot
- scripts/__init__.py
- scripts/_common.py
- scripts/check_deck_geometry.py
- scripts/generate_simulation_plan.py
- scripts/inspect_backends.py
- scripts/plan_transfers.py
- scripts/validate_manifest.py
- pymatgen
- scripts/_common.py
- scripts/artifact_manifest.py
- scripts/composition_structure_validator.py
- scripts/io_conversion_plan.py
- scripts/mp_query.py
- scripts/phase_diagram_generator.py
- scripts/structure_analyzer.py
- scripts/structure_converter.py
- scripts/symmetry_sensitivity_report.py
- pymc
- assets/hierarchical_model_template.py
- assets/linear_regression_template.py
- scripts/model_comparison.py
- scripts/model_diagnostics.py
- pymoo
- scripts/custom_problem_example.py
- scripts/decision_making_example.py
- scripts/many_objective_example.py
- scripts/multi_objective_example.py
- scripts/single_objective_example.py
- pyopenms
- scripts/_common.py
- scripts/accurate_mass_search.py
- scripts/align_link_quantify.py
- scripts/consensus_to_matrix.py
- scripts/convert_format.py
- scripts/detect_adducts.py
- scripts/detect_features_centroided.py
- scripts/detect_features_metabo.py
- scripts/digest_protein.py
- scripts/export_gnps_sirius.py
- scripts/extract_chromatograms.py
- scripts/inspect_ms_data.py
- scripts/mass_calculator.py
- scripts/plot_ms_data.py
- scripts/process_identifications.py
- scripts/process_spectra.py
- scripts/theoretical_spectrum.py
- pysam
- scripts/alignment_qc.py
- scripts/filter_alignments.py
- scripts/inspect_hts.py
- scripts/variant_summary.py
- pytdc
- scripts/_common.py
- scripts/benchmark_evaluation.py
- scripts/cache_audit.py
- scripts/discover_metadata.py
- scripts/load_and_split_data.py
- scripts/molecular_generation.py
- pytorch-lightning
- scripts/quick_trainer_setup.py
- scripts/template_datamodule.py
- scripts/template_lightning_module.py
- qiime2-amplicon
- scripts/amplicon_workflow.py
- qiskit
- scripts/check_environment.py
- scripts/inspect_runtime.py
- scripts/run_local_primitives.py
- qutip
- scripts/_common.py
- scripts/convergence_sweep.py
- scripts/qobj_model_validator.py
- scripts/result_audit.py
- scripts/solver_config_planner.py
- scripts/steady_state_spectrum_planner.py
- scripts/two_level_simulation.py
- rdkit
- scripts/_common.py
- scripts/molecular_properties.py
- scripts/similarity_search.py
- scripts/substructure_filter.py
- relion
- scripts/spa_workflow.py
- relsa-severity-assessment
- scripts/_common.py
- scripts/forecast_relsa.py
- scripts/kde_thresholds.py
- scripts/relsa_score.py
- research-lookup
- scripts/manuscript_packet.py
- scripts/research_lookup.py
- scanpy
- assets/analysis_template.py
- scripts/_common.py
- scripts/annotate.py
- scripts/batch_correct.py
- scripts/cluster.py
- scripts/convert.py
- scripts/find_markers.py
- scripts/inspect_data.py
- scripts/plot.py
- scripts/preprocess.py
- scripts/pseudobulk.py
- scripts/qc_analysis.py
- scripts/reduce_dimensions.py
- scripts/run_pipeline.py
- scripts/score_genes.py
- scripts/subset.py
- scholar-evaluation
- scripts/_common.py
- scripts/calculate_scores.py
- scripts/check_process.py
- scripts/check_traceability.py
- scripts/generate_report_scaffold.py
- scripts/summarize_agreement.py
- scripts/validate_rubric.py
- scripts/weight_sensitivity.py
- scientific-brainstorming
- scripts/_common.py
- scripts/evaluate_matrix.py
- scripts/session_scaffold.py
- scripts/validate_register.py
- scientific-schematics
- scripts/example_usage.sh
- scripts/generate_schematic.py
- scripts/generate_schematic_ai.py
- scientific-slides
- scripts/generate_schematic.py
- scripts/generate_schematic_ai.py
- scripts/generate_slide_image.py
- scripts/generate_slide_image_ai.py
- scripts/pdf_to_images.py
- scripts/slides_to_pdf.py
- scripts/validate_presentation.py
- scientific-visualization
- assets/color_palettes.py
- scripts/_common.py
- scripts/export_plan.py
- scripts/figure_export.py
- scripts/image_metadata.py
- scripts/palette_audit.py
- scripts/style_presets.py
- scripts/style_preview.py
- scientific-writing
- scripts/_common.py
- scripts/audit_claims.py
- scripts/check_consistency.py
- scripts/check_references.py
- scripts/lint_manuscript.py
- scripts/scaffold_manuscript.py
- scripts/select_reporting_guidelines.py
- scripts/validate_authorship.py
- scripts/validate_manifest.py
- scikit-learn
- scripts/classification_pipeline.py
- scripts/clustering_analysis.py
- scikit-survival
- scripts/_common.py
- scripts/competing_risk_cif.py
- scripts/evaluate_survival_metrics.py
- scripts/model_report.py
- scripts/train_survival_model.py
- scripts/validate_survival_csv.py
- scvelo
- scripts/rna_velocity_workflow.py
- shap
- scripts/tabular_report.py
- simpy
- scripts/_common.py
- scripts/basic_simulation_template.py
- scripts/bounded_queue_scenario.py
- scripts/event_trace_summary.py
- scripts/replication_runner.py
- scripts/resource_monitor.py
- scripts/validate_simulation_config.py
- stable-baselines3
- scripts/custom_env_template.py
- scripts/evaluate_agent.py
- scripts/train_rl_agent.py
- statistical-analysis
- scripts/assumption_checks.py
- statistical-power
- scripts/power.py
- scripts/simulate_power.py
- tellurium
- scripts/kinetic_experiment.py
- timesfm-forecasting
- examples/anomaly-detection/detect_anomalies.py
- examples/covariates-forecasting/demo_covariates.py
- examples/global-temperature/generate_animation_data.py
- examples/global-temperature/generate_gif.py
- examples/global-temperature/generate_html.py
- examples/global-temperature/run_example.sh
- examples/global-temperature/run_forecast.py
- examples/global-temperature/visualize_forecast.py
- scripts/check_system.py
- scripts/forecast_csv.py
- treatment-plans
- scripts/_common.py
- scripts/check_completeness.py
- scripts/check_consistency.py
- scripts/generate_template.py
- scripts/privacy_process_check.py
- scripts/timeline_generator.py
- scripts/validate_traceability.py
- scripts/validate_treatment_plan.py
- uncertainty-and-units
- scripts/_common.py
- scripts/audit_units.py
- scripts/check_plausibility.py
- scripts/convert_units.py
- scripts/format_result.py
- scripts/propagate_uncertainty.py
- scripts/uncertainty_budget.py
- venue-templates
- scripts/customize_template.py
- scripts/query_template.py
- scripts/validate_format.py
- waypoint-bio
- scripts/profiler_to_waypoint.py
- scripts/vocab_coverage.py

plugin.json

name: scientific-agent-skills
version: 2.72.0
description: Ready-to-use scientific and research Agent Skills for biology, chemistry, medicine, and related workflows.
author: K-Dense Inc.https://k-dense.ai
license: MIT
homepage: https://github.com/K-Dense-AI/scientific-agent-skills
repository: https://github.com/K-Dense-AI/scientific-agent-skills
keywords: agent-skills science research bioinformatics cheminformatics biology chemistry medicine

plugin.json

{
  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
  "name": "scientific-agent-skills",
  "version": "2.72.0",
  "description": "Ready-to-use scientific and research Agent Skills for biology, chemistry, medicine, and related workflows.",
  "author": {
    "name": "K-Dense Inc.",
    "url": "https://k-dense.ai"
  },
  "homepage": "https://github.com/K-Dense-AI/scientific-agent-skills",
  "repository": "https://github.com/K-Dense-AI/scientific-agent-skills",
  "license": "MIT",
  "keywords": [
    "agent-skills",
    "science",
    "research",
    "bioinformatics",
    "cheminformatics",
    "biology",
    "chemistry",
    "medicine"
  ]
}

What else this package ships

These files come with the package and this site does not publish them. They are listed so you know what is there before you install it.

531Python files
3shell scripts
2JavaScript files
89JSON files
17data files
6YAML files
5text files
30other files

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