pyedger 0.1.0__tar.gz

pyedger-0.1.0/LICENSE

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+GNU LESSER GENERAL PUBLIC LICENSE
+Version 3, 29 June 2007
+
+This Python port is released under LGPL-3.0-or-later, matching the
+license of the upstream Bioconductor package it ports. The full
+LGPL-3 text is at https://www.gnu.org/licenses/lgpl-3.0.txt and
+applies to all files in this repository.

pyedger-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyedger
+Version: 0.1.0
+Summary: Pure-Python port of Bioconductor edgeR — negative-binomial models for differential expression of count data (estimateDisp, glmFit, glmLRT, glmQLFTest, exactTest).
+Author-email: Zehua Zeng <starlitnightly@163.com>
+License: LGPL-3.0-or-later
+Project-URL: Homepage, https://github.com/omicverse/py-edgeR
+Project-URL: Repository, https://github.com/omicverse/py-edgeR
+Project-URL: Issues, https://github.com/omicverse/py-edgeR/issues
+Project-URL: Upstream Bioc package, https://bioconductor.org/packages/release/bioc/html/edgeR.html
+Project-URL: Upstream (omicverse), https://github.com/Starlitnightly/omicverse
+Keywords: edgeR,differential-expression,RNA-seq,count-data,negative-binomial,GLM,dispersion,bioinformatics
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Requires-Dist: scipy>=1.10
+Requires-Dist: pandas>=1.5
+Provides-Extra: dev
+Requires-Dist: pytest>=7; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Dynamic: license-file
+
+# pyedger
+
+A **pure-Python port of [Bioconductor edgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html)** (Robinson, McCarthy & Smyth, *Bioinformatics* 2010) — negative-binomial models for differential expression of count data.
+
+- **No `rpy2`**, no R install — the edgeR negative-binomial GLM workflow reimplemented in NumPy / SciPy
+- The canonical pipelines: `DGEList → calcNormFactors → estimateDisp → glmQLFit → glmQLFTest` and the classic `exactTest`
+- TMM normalization, common / trended / tagwise dispersion, GLM and quasi-likelihood F-tests, `filterByExpr`, `cpm` / `aveLogCPM`
+- Both Python-style (`glm_fit`, `estimate_disp`, `top_tags`) and R-style (`glmFit`, `estimateDisp`, `topTags`) names exported
+
+> This is a **standalone mirror** of the implementation developed in [`omicverse`](https://github.com/Starlitnightly/omicverse), where it powers the edgeR differential-expression backend of `ov.bulk` / `pyDEG`.
+
+## Install
+
+```bash
+pip install pyedger
+```
+
+## Quick start
+
+```python
+import numpy as np
+import pyedger
+
+# counts: genes x samples raw count matrix; group: per-sample condition labels
+dge = pyedger.DGEList(counts=counts, group=group)
+dge = pyedger.calcNormFactors(dge)                       # TMM normalization
+keep = pyedger.filterByExpr(dge, group=group)
+dge = dge[keep]
+
+# Quasi-likelihood F-test workflow (the recommended edgeR pipeline)
+dge = pyedger.estimateDisp(dge, design)
+fit = pyedger.glmQLFit(dge, design)
+qlf = pyedger.glmQLFTest(fit, coef=1)
+res = pyedger.topTags(qlf, n=np.inf)
+res.head()
+```
+
+### Classic exact test
+
+```python
+dge = pyedger.estimateDisp(dge, design)
+et = pyedger.exactTest(dge, pair=("control", "treated"))
+pyedger.topTags(et)
+```
+
+## API
+
+| Python | R counterpart |
+|---|---|
+| `DGEList` | `DGEList` |
+| `calc_norm_factors` / `calcNormFactors` | `calcNormFactors` (TMM) |
+| `filter_by_expr` / `filterByExpr` | `filterByExpr` |
+| `estimate_disp` / `estimateDisp` | `estimateDisp` |
+| `glm_fit` / `glmFit`, `glm_lrt` / `glmLRT` | `glmFit`, `glmLRT` |
+| `glm_ql_fit` / `glmQLFit`, `glm_qlf_test` / `glmQLFTest` | `glmQLFit`, `glmQLFTest` |
+| `exact_test` / `exactTest` | `exactTest` |
+| `glm_treat` / `glmTreat` | `glmTreat` |
+| `cpm`, `ave_log_cpm` / `aveLogCPM` | `cpm`, `aveLogCPM` |
+| `top_tags` / `topTags` | `topTags` |
+| `decide_tests_dge` / `decideTests` | `decideTestsDGE` |
+| `DGEGLM`, `DGELRT`, `DGEExact`, `TestResults` | the corresponding S4 classes |
+
+## Citation
+
+> Robinson, M.D., McCarthy, D.J., Smyth, G.K. **edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.** *Bioinformatics* 26(1), 139–140 (2010).
+
+…and acknowledge omicverse / this repo for the Python port.
+
+## License
+
+LGPL-3.0-or-later — matches the upstream Bioconductor package.

pyedger-0.1.0/README.md

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+# pyedger
+
+A **pure-Python port of [Bioconductor edgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html)** (Robinson, McCarthy & Smyth, *Bioinformatics* 2010) — negative-binomial models for differential expression of count data.
+
+- **No `rpy2`**, no R install — the edgeR negative-binomial GLM workflow reimplemented in NumPy / SciPy
+- The canonical pipelines: `DGEList → calcNormFactors → estimateDisp → glmQLFit → glmQLFTest` and the classic `exactTest`
+- TMM normalization, common / trended / tagwise dispersion, GLM and quasi-likelihood F-tests, `filterByExpr`, `cpm` / `aveLogCPM`
+- Both Python-style (`glm_fit`, `estimate_disp`, `top_tags`) and R-style (`glmFit`, `estimateDisp`, `topTags`) names exported
+
+> This is a **standalone mirror** of the implementation developed in [`omicverse`](https://github.com/Starlitnightly/omicverse), where it powers the edgeR differential-expression backend of `ov.bulk` / `pyDEG`.
+
+## Install
+
+```bash
+pip install pyedger
+```
+
+## Quick start
+
+```python
+import numpy as np
+import pyedger
+
+# counts: genes x samples raw count matrix; group: per-sample condition labels
+dge = pyedger.DGEList(counts=counts, group=group)
+dge = pyedger.calcNormFactors(dge)                       # TMM normalization
+keep = pyedger.filterByExpr(dge, group=group)
+dge = dge[keep]
+
+# Quasi-likelihood F-test workflow (the recommended edgeR pipeline)
+dge = pyedger.estimateDisp(dge, design)
+fit = pyedger.glmQLFit(dge, design)
+qlf = pyedger.glmQLFTest(fit, coef=1)
+res = pyedger.topTags(qlf, n=np.inf)
+res.head()
+```
+
+### Classic exact test
+
+```python
+dge = pyedger.estimateDisp(dge, design)
+et = pyedger.exactTest(dge, pair=("control", "treated"))
+pyedger.topTags(et)
+```
+
+## API
+
+| Python | R counterpart |
+|---|---|
+| `DGEList` | `DGEList` |
+| `calc_norm_factors` / `calcNormFactors` | `calcNormFactors` (TMM) |
+| `filter_by_expr` / `filterByExpr` | `filterByExpr` |
+| `estimate_disp` / `estimateDisp` | `estimateDisp` |
+| `glm_fit` / `glmFit`, `glm_lrt` / `glmLRT` | `glmFit`, `glmLRT` |
+| `glm_ql_fit` / `glmQLFit`, `glm_qlf_test` / `glmQLFTest` | `glmQLFit`, `glmQLFTest` |
+| `exact_test` / `exactTest` | `exactTest` |
+| `glm_treat` / `glmTreat` | `glmTreat` |
+| `cpm`, `ave_log_cpm` / `aveLogCPM` | `cpm`, `aveLogCPM` |
+| `top_tags` / `topTags` | `topTags` |
+| `decide_tests_dge` / `decideTests` | `decideTestsDGE` |
+| `DGEGLM`, `DGELRT`, `DGEExact`, `TestResults` | the corresponding S4 classes |
+
+## Citation
+
+> Robinson, M.D., McCarthy, D.J., Smyth, G.K. **edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.** *Bioinformatics* 26(1), 139–140 (2010).
+
+…and acknowledge omicverse / this repo for the Python port.
+
+## License
+
+LGPL-3.0-or-later — matches the upstream Bioconductor package.

pyedger-0.1.0/pyedger/__init__.py

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+"""Pure-Python subset of Bioconductor edgeR."""
+
+from .core import (
+    DGEExact,
+    DGEGLM,
+    DGELRT,
+    DGEList,
+    TestResults,
+    add_prior_count,
+    ave_log_cpm,
+    calc_norm_factors,
+    cpm,
+    decide_tests_dge,
+    effective_lib_sizes,
+    equalize_lib_sizes,
+    estimate_common_disp,
+    estimate_disp,
+    estimate_glm_common_disp,
+    estimate_glm_tagwise_disp,
+    estimate_glm_trended_disp,
+    estimate_tagwise_disp,
+    exact_test,
+    filter_by_expr,
+    glm_fit,
+    glm_lrt,
+    glm_ql_fit,
+    glm_qlf_test,
+    glm_treat,
+    pred_fc,
+    top_tags,
+)
+
+calcNormFactors = calc_norm_factors
+effectiveLibSizes = effective_lib_sizes
+equalizeLibSizes = equalize_lib_sizes
+estimateCommonDisp = estimate_common_disp
+estimateTagwiseDisp = estimate_tagwise_disp
+estimateDisp = estimate_disp
+estimateGLMCommonDisp = estimate_glm_common_disp
+estimateGLMTagwiseDisp = estimate_glm_tagwise_disp
+estimateGLMTrendedDisp = estimate_glm_trended_disp
+exactTest = exact_test
+filterByExpr = filter_by_expr
+glmFit = glm_fit
+glmLRT = glm_lrt
+glmTreat = glm_treat
+glmQLFit = glm_ql_fit
+glmQLFTest = glm_qlf_test
+predFC = pred_fc
+addPriorCount = add_prior_count
+decideTestsDGE = decide_tests_dge
+decideTests = decide_tests_dge
+topTags = top_tags
+aveLogCPM = ave_log_cpm
+
+__all__ = [
+    "DGEExact",
+    "DGEGLM",
+    "DGELRT",
+    "DGEList",
+    "TestResults",
+    "add_prior_count",
+    "addPriorCount",
+    "ave_log_cpm",
+    "aveLogCPM",
+    "calc_norm_factors",
+    "calcNormFactors",
+    "effective_lib_sizes",
+    "effectiveLibSizes",
+    "equalize_lib_sizes",
+    "equalizeLibSizes",
+    "estimate_common_disp",
+    "estimateCommonDisp",
+    "estimate_tagwise_disp",
+    "estimateTagwiseDisp",
+    "estimate_disp",
+    "estimateDisp",
+    "estimate_glm_common_disp",
+    "estimateGLMCommonDisp",
+    "estimate_glm_tagwise_disp",
+    "estimateGLMTagwiseDisp",
+    "estimate_glm_trended_disp",
+    "estimateGLMTrendedDisp",
+    "exact_test",
+    "exactTest",
+    "filter_by_expr",
+    "filterByExpr",
+    "glm_fit",
+    "glmFit",
+    "glm_lrt",
+    "glmLRT",
+    "glm_treat",
+    "glmTreat",
+    "glm_ql_fit",
+    "glmQLFit",
+    "glm_qlf_test",
+    "glmQLFTest",
+    "pred_fc",
+    "predFC",
+    "top_tags",
+    "topTags",
+    "cpm",
+    "decide_tests_dge",
+    "decideTests",
+    "decideTestsDGE",
+]