py-sparkx-omicverse 0.1.0__tar.gz

py_sparkx_omicverse-0.1.0/ATTRIBUTION.md

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+# Attribution
+
+Upstream SPARK 1.1.1, commit a8b4bf27b804604dfda53da42992f100b8e4e727.
+Algorithms reconstructed from the upstream source under the accompanying LICENSE.
+Upstream author declarations:
+
+```
+Package: SPARK
+Type: Package
+Title: Spatial Pattern Recognition via Kernels
+Version: 1.1.1
+Date: 2021-02-18
+Author: Shiquan Sun, Jiaqiang Zhu, and Xiang Zhou
+Maintainer: Jiaqiang Zhu <jiaqiang@umich.edu>
+Description: SPARK is an efficient tool for identifying spatial expression patterns. SPARK directly models raw count data generated from various spatial resolved transcriptomic techniques. With a new efficient penalized quasi-likelihood based algorithm, SPARK is scalable to data sets with tens of thousands of genes measured on thousands of samples. Build upon a non-parametric framework, SPARK-X is scalable to large-scale data sets with tens of thousands of genes measured on hundred thousands of samples.
+License: GPL-3
+Depends: R (>= 3.4.0), methods
+Imports: Rcpp (>= 1.0.5),foreach,doParallel,parallel,Matrix,CompQuadForm,matlab,pracma
+LinkingTo: Rcpp, RcppArmadillo
+RoxygenNote: 7.1.1
+
+```
+
+The central Davies implementation also follows cran/CompQuadForm src/qfc.cpp at f1e110ac54aa0e64dda8cf6254823e801878e036, Algorithm AS 155 by Robert B. Davies (1980). GPL-compatible attribution retained in _davies.py.

py_sparkx_omicverse-0.1.0/AUDIT.md

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+# Reviewed R function coverage
+
+AUDIT_AUTO.md is generated by rebuildr. This table also handles exportPattern and comma-separated exportMethods manually.
+
+| R export | Python | Scope |
+|---|---|---|
+| ACAT | pysparkx.acat | SPARK-X single and mixture projection kernels, covariates, ACAT and BY. No SPARK generalized linear spatial mixed models, normalization suite or arbitrary quadratic-form API. |
+| CombinePValues | - | Outside initial scope |
+| ComputeGaussianL | - | Outside initial scope |
+| ComputeGaussianPL | - | Outside initial scope |
+| ComputeTestQuantRcpp_Gaussian | - | Outside initial scope |
+| ComputeTestQuantRcpp_cov | - | Outside initial scope |
+| ComputeTestQuantRcpp_nocov | - | Outside initial scope |
+| ComputeWeightsRcpp | - | Outside initial scope |
+| CovariatesAI | - | Outside initial scope |
+| CreateSPARKObject | - | Outside initial scope |
+| ED_cpp | - | Outside initial scope |
+| FilteringGenesCells | - | Outside initial scope |
+| NormalizeVST | - | Outside initial scope |
+| NormalizeVSTfast | - | Outside initial scope |
+| SparseSysMatEigen | - | Outside initial scope |
+| SysMatEigen | - | Outside initial scope |
+| noCovariatesAI | - | Outside initial scope |
+| rcpparma_bothproducts | - | Outside initial scope |
+| rcpparma_hello_world | - | Outside initial scope |
+| rcpparma_innerproduct | - | Outside initial scope |
+| rcpparma_outerproduct | - | Outside initial scope |
+| sp_means_Rcpp | - | Outside initial scope |
+| sp_nz_count_Rcpp | - | Outside initial scope |
+| sp_sums_Rcpp | - | Outside initial scope |
+| sp_vars_Rcpp | - | Outside initial scope |
+| spark.ai | - | Outside initial scope |
+| spark.fit | - | Outside initial scope |
+| spark.test | - | Outside initial scope |
+| spark.test_each | - | Outside initial scope |
+| spark.vc | - | Outside initial scope |
+| spark.weights | - | Outside initial scope |
+| sparkg_sw | - | Outside initial scope |
+| sparkg_sw_sk | - | Outside initial scope |
+| sparkx | pysparkx.sparkx | SPARK-X single and mixture projection kernels, covariates, ACAT and BY. No SPARK generalized linear spatial mixed models, normalization suite or arbitrary quadratic-form API. |
+| sparkx.sk | - | Outside initial scope |
+| sparkx.sksg | - | Outside initial scope |
+| sparkx_pval | - | Outside initial scope |
+| transloc_func | - | Outside initial scope |

py_sparkx_omicverse-0.1.0/AUDIT_AUTO.md

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+## R function coverage audit
+
+### Coverage summary
+
+| Category | Ported | Total | % |
+|---|---|---|---|
+| Exported R functions | 0 | 0 | 0.0% |
+| Internal helpers (reachable) | 0 | 0 | 0.0% |
+
+_Python package exposes 0 unique names._
+
+### Exported R functions
+
+| R function | Python equivalent | Status |
+|---|---|---|
+
+### Internal helpers reachable from exports
+
+| R helper | File | Python equivalent | Status |
+|---|---|---|---|

py_sparkx_omicverse-0.1.0/DISCOVERY.md

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+# Discovery: SPARK
+
+Checked omicverse organization repository inventory on 2026-11-11: no standalone target port found.
+Upstream commit: `a8b4bf27b804604dfda53da42992f100b8e4e727`.
+Scope: sparkx; other package functions are excluded.
+
+Reuse: NumPy/SciPy/pandas for matrix and SVD/NNLS operations. muscat uses existing pyedger and python-limma rather than rewriting either statistical engine.
+RUVg already exists in omicverse PR #1035 and will be extracted with its reference tests rather than independently duplicated.
+Nebulosa and scran pooling have external candidates and are separate reuse audits, not new ports.
+
+Fixed numerical gates are in manifest.yaml, committed before implementation. Synthetic and real public fixtures will be distinguished. No biological accuracy claim follows from fixture-level equivalence.