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herry423/bionexus-reliability

v1.0.0-rc.8Apache-2.0

Scientific Reliability Layer for AI-Assisted Biology. Know what your evidence actually warrants: pre-submission shadow review of multi-donor single-cell differential expression, evidence gap location, and human scientific review support.

GitHub

commands

  • python

scripts

  • external-evidence-audit
  • scripts/assess_ecosystem_claim.py
  • scripts/audit_external_evidence.py
  • instrument-data-to-allotrope
  • scripts/convert_to_asm.py
  • scripts/export_parser.py
  • scripts/flatten_asm.py
  • scripts/validate_asm.py
  • scripts/yaml_mapping_engine.py
  • nextflow-development
  • 59 more
    • scripts/check_environment.py
    • scripts/cluster_profile_generator.py
    • scripts/detect_data_type.py
    • scripts/generate_samplesheet.py
    • scripts/manage_genomes.py
    • scripts/nfcore_launch.py
    • scripts/sra_geo_fetch.py
    • scripts/utils/__init__.py
    • scripts/utils/file_discovery.py
    • scripts/utils/ncbi_utils.py
    • scripts/utils/sample_inference.py
    • scripts/utils/validators.py
    • provenance-and-audit
    • scripts/_common.py
    • scripts/methods_generator.py
    • scripts/provenance_tracker.py
    • scvi-tools
    • scripts/cluster_embed.py
    • scripts/differential_expression.py
    • scripts/hyperparam_search.py
    • scripts/integrate_datasets.py
    • scripts/model_utils.py
    • scripts/prepare_data.py
    • scripts/scvi_smoke.py
    • scripts/train_model.py
    • scripts/transfer_labels.py
    • scripts/validate_adata.py
    • single-cell-rna-qc
    • scripts/_common.py
    • scripts/ambient_rna.py
    • scripts/doublet_detection.py
    • scripts/qc_analysis.py
    • scripts/qc_core.py
    • scripts/qc_plotting.py
    • scripts/scrna_cluster_stability.py
    • scripts/scrna_convert.py
    • scripts/scrna_deseq.py
    • scripts/scrna_inspect.py
    • scripts/scrna_integrate.py
    • scripts/scrna_markers.py
    • scripts/scrna_pipeline.py
    • scripts/scrna_plot.py
    • scripts/scrna_preprocess.py
    • scripts/scrna_pseudobulk.py
    • scripts/scrna_reduce_cluster.py
    • scripts/scrna_scrublet.py
    • scripts/scrna_subset.py
    • spatial-transcriptomics
    • scripts/_common.py
    • scripts/spatial_clustering.py
    • scripts/spatial_deconvolution.py
    • scripts/spatial_inspect.py
    • scripts/spatial_io.py
    • scripts/spatial_niche_analysis.py
    • scripts/spatial_pipeline.py
    • scripts/spatial_plot.py
    • scripts/spatial_preprocessing.py
    • scripts/spatial_variable_genes.py
    • scripts/spatial_visualization.py
plugin.json
name
bionexus-reliability
version
1.0.0-rc.8
description
Scientific Reliability Layer for AI-Assisted Biology. Know what your evidence actually warrants: pre-submission shadow review of multi-donor single-cell differential expression, evidence gap location, and human scientific review support.
author
BioNexus Team
license
Apache-2.0
keywords
bionexusscientific-reliabilitywarrant-enginebioinformaticssingle-celldifferential-expressionpseudobulkreproducibilitymcp
mcp.json
  • bionexus-local-mcpstdiopython ${PLUGIN_ROOT}/scripts/local_mcp_server.py --audit-log ${PLUGIN_ROOT}/.bionexus-audit/mcp-host-audit.jsonl

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.

  • 105Python files
  • 17YAML files
  • 6text files
  • 2JSON files
  • LICENSE
View on GitHub

Fields the format does not define

This package's plugin.json declares these at its top level. The Agent Plugins format gives them no meaning, so a client loads the plugin and ignores them.

  • skills
  • mcpServers