openomicsbench 1.0.3__py3-none-any.whl

omicsbench/__init__.py

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+"""Discovery, retrieval and validation of transcriptomics objects."""
+__version__ = "1.0.3"

omicsbench/__main__.py

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+from .cli import main
+main()

omicsbench/_collection/datasets/rnaseq/fixture-001/LICENSE-DATA.md

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+# Fixture data rights
+
+These numerical arrays are generated by the project workflow. They contain no third-party observations. The generator is provided with the source code; project licensing must be confirmed by the owner before public release. Local testing is the intended use of this development snapshot.

omicsbench/_collection/datasets/rnaseq/fixture-001/README.md

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+# Synthetic RNA infrastructure fixture
+
+Eight generated libraries exercise parsing, sample order, feature reduction, batch design and cache integrity. No patient or experimental data are included.
+
+Run `omicsbench validate fixture-001` from the repository root. Both data tiers contain the smallest candidate that passes the diagnostic profile; they deliberately share content. This fixture is smaller than a normal pocket and is excluded from the biological collection count.
+
+The baseline fits log2(CPM + 1) to condition and batch. It does not calculate differential-expression p-values and is not a DESeq2 substitute. Exact sample order and unchanged integer counts are mandatory. Thresholds and the complete candidate curve are stored under expected.
+
+The generator and seed are recorded in provenance/transform.json. Cite the software version when reporting a test; do not cite this fixture as a biological study.

omicsbench/_collection/datasets/rnaseq/fixture-001/expected/baseline.json

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+{
+  "contrast": "treated - control",
+  "explained_variance": [
+    0.4023170757,
+    0.1144947139
+  ],
+  "libraries": [
+    107781.0,
+    105880.0,
+    120052.0,
+    122481.0,
+    136629.0,
+    136369.0,
+    160265.0,
+    156240.0
+  ],
+  "method": "OLS on log2(CPM+1), condition plus batch; diagnostic only",
+  "pca": [
+    [
+      22.8705190742,
+      23.2787540551
+    ],
+    [
+      21.9559967987,
+      -19.0750880714
+    ],
+    [
+      23.9940716755,
+      -9.2731817474
+    ],
+    [
+      22.2559894323,
+      5.1532379393
+    ],
+    [
+      -23.4029150581,
+      2.0461524501
+    ],
+    [
+      -22.1524861912,
+      -10.941973144
+    ],
+    [
+      -22.3717864914,
+      4.7776117217
+    ],
+    [
+      -23.1493892399,
+      4.0344867966
+    ]
+  ],
+  "sample_ids": [
+    "control1",
+    "control2",
+    "control3",
+    "control4",
+    "treated1",
+    "treated2",
+    "treated3",
+    "treated4"
+  ]
+}

omicsbench/_collection/datasets/rnaseq/fixture-001/expected/size-fidelity.json

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+[
+  {
+    "features": 256,
+    "metrics": {
+      "distance_correlation": 0.8667927827,
+      "sign_concordance": 1.0,
+      "spearman_logfc": 0.9989249542,
+      "top_k_jaccard": 0.9230769231
+    },
+    "pass": false
+  },
+  {
+    "features": 512,
+    "metrics": {
+      "distance_correlation": 0.9265055624,
+      "sign_concordance": 0.9958932238,
+      "spearman_logfc": 0.9993942655,
+      "top_k_jaccard": 0.8181818182
+    },
+    "pass": true
+  },
+  {
+    "features": 1024,
+    "metrics": {
+      "distance_correlation": 0.9954390989,
+      "sign_concordance": 0.9906832298,
+      "spearman_logfc": 0.9996573922,
+      "top_k_jaccard": 0.8181818182
+    },
+    "pass": true
+  },
+  {
+    "features": 1536,
+    "metrics": {
+      "distance_correlation": 0.9975214954,
+      "sign_concordance": 1.0,
+      "spearman_logfc": 0.9999186827,
+      "top_k_jaccard": 0.8518518519
+    },
+    "pass": true
+  },
+  {
+    "features": 2000,
+    "metrics": {
+      "distance_correlation": 1.0,
+      "sign_concordance": 1.0,
+      "spearman_logfc": 1.0,
+      "top_k_jaccard": 1.0
+    },
+    "pass": true
+  }
+]