exprmat 0.1.26__tar.gz → 0.1.27__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (169) hide show
  1. {exprmat-0.1.26 → exprmat-0.1.27}/PKG-INFO +1 -1
  2. {exprmat-0.1.26 → exprmat-0.1.27}/pyproject.toml +5 -1
  3. exprmat-0.1.26/exprmat/data/tools/gene-model.ipynb +0 -685
  4. exprmat-0.1.26/exprmat/data/tools/retrieve-assembly-info.ipynb +0 -1882
  5. {exprmat-0.1.26 → exprmat-0.1.27}/Cargo.lock +0 -0
  6. {exprmat-0.1.26 → exprmat-0.1.27}/Cargo.toml +0 -0
  7. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/__init__.py +0 -0
  8. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/ansi.py +0 -0
  9. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/clustering/__init__.py +0 -0
  10. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/clustering/cnmf.py +0 -0
  11. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/clustering/dbscan.py +0 -0
  12. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/clustering/kmeans.py +0 -0
  13. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/clustering/leiden.py +0 -0
  14. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/clustering/nmf.py +0 -0
  15. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/clustering/rogue.py +0 -0
  16. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/clustering/seriation.py +0 -0
  17. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/clustering/spectral.py +0 -0
  18. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/clustering/utils.py +0 -0
  19. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/cnv/__init__.py +0 -0
  20. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/cnv/cnvscore.py +0 -0
  21. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/cnv/infercnv.py +0 -0
  22. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/configuration.py +0 -0
  23. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/__init__.py +0 -0
  24. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/cistarget.py +0 -0
  25. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/delim.py +0 -0
  26. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/finders.py +0 -0
  27. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/geneset.py +0 -0
  28. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/gff.py +0 -0
  29. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/io.py +0 -0
  30. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/lr.py +0 -0
  31. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/presets.py +0 -0
  32. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/private.py +0 -0
  33. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/ranges.py +0 -0
  34. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/signature.py +0 -0
  35. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/data/tf.py +0 -0
  36. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/descriptive/__init__.py +0 -0
  37. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/descriptive/aggregate.py +0 -0
  38. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/descriptive/atac.py +0 -0
  39. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/descriptive/aucell.py +0 -0
  40. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/descriptive/de.py +0 -0
  41. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/descriptive/gse.py +0 -0
  42. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/descriptive/kde.py +0 -0
  43. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/descriptive/recovery.py +0 -0
  44. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/descriptive/summary.py +0 -0
  45. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/descriptive/tcr.py +0 -0
  46. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/dynamics/__init__.py +0 -0
  47. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/dynamics/generank.py +0 -0
  48. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/dynamics/linreg.py +0 -0
  49. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/dynamics/moments.py +0 -0
  50. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/dynamics/optimization.py +0 -0
  51. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/dynamics/parallel.py +0 -0
  52. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/dynamics/preprocess.py +0 -0
  53. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/dynamics/pseudotime.py +0 -0
  54. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/dynamics/transition.py +0 -0
  55. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/dynamics/utils.py +0 -0
  56. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/dynamics/velocity.py +0 -0
  57. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/grn/__init__.py +0 -0
  58. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/grn/infergrn.py +0 -0
  59. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/grn/modules.py +0 -0
  60. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/grn/prune.py +0 -0
  61. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/grn/regressors.py +0 -0
  62. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/grn/utils.py +0 -0
  63. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/__init__.py +0 -0
  64. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/aggregate.py +0 -0
  65. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/method.py +0 -0
  66. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/methods/__init__.py +0 -0
  67. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/methods/cellchat.py +0 -0
  68. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/methods/cellphonedb.py +0 -0
  69. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/methods/connectome.py +0 -0
  70. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/methods/geomean.py +0 -0
  71. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/methods/logfc.py +0 -0
  72. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/methods/natmi.py +0 -0
  73. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/methods/rank_aggregate.py +0 -0
  74. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/methods/scseqcomm.py +0 -0
  75. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/methods/singlecellsignalr.py +0 -0
  76. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/pipeline.py +0 -0
  77. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/preprocess.py +0 -0
  78. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/resources.py +0 -0
  79. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/lr/utils.py +0 -0
  80. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/__init__.py +0 -0
  81. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/atac.py +0 -0
  82. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/cnmf.py +0 -0
  83. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/cnv.py +0 -0
  84. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/de.py +0 -0
  85. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/expression.py +0 -0
  86. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/gse.py +0 -0
  87. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/lr.py +0 -0
  88. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/palettes.py +0 -0
  89. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/sankey.py +0 -0
  90. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/summary.py +0 -0
  91. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/track.py +0 -0
  92. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/utils.py +0 -0
  93. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/plotting/velocity.py +0 -0
  94. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/__init__.py +0 -0
  95. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/doublets/__init__.py +0 -0
  96. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/doublets/composite.py +0 -0
  97. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/doublets/scrublet.py +0 -0
  98. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/emptydrops.py +0 -0
  99. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/filter.py +0 -0
  100. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/impute/__init__.py +0 -0
  101. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/impute/magic.py +0 -0
  102. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/integrate.py +0 -0
  103. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/linear.py +0 -0
  104. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/normal.py +0 -0
  105. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/plot.py +0 -0
  106. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/qc.py +0 -0
  107. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/sctransform/__init__.py +0 -0
  108. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/sctransform/estimate.py +0 -0
  109. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/sctransform/ksmooth.py +0 -0
  110. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/sctransform/residual.py +0 -0
  111. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/sctransform/transform.py +0 -0
  112. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/sparse.py +0 -0
  113. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/preprocessing/uniform.py +0 -0
  114. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reader/__init__.py +0 -0
  115. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reader/experiment.py +0 -0
  116. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reader/matcher.py +0 -0
  117. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reader/metadata.py +0 -0
  118. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reader/peaks.py +0 -0
  119. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reader/static.py +0 -0
  120. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reduction/__init__.py +0 -0
  121. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reduction/forceatlas.py +0 -0
  122. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reduction/mde.py +0 -0
  123. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reduction/nn.py +0 -0
  124. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reduction/outliers.py +0 -0
  125. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reduction/pca.py +0 -0
  126. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reduction/plot.py +0 -0
  127. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reduction/spectral.py +0 -0
  128. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reduction/tsne.py +0 -0
  129. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/reduction/umap.py +0 -0
  130. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/trajectory/pcurve.py +0 -0
  131. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/transfer/__init__.py +0 -0
  132. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/transfer/atlas.py +0 -0
  133. {exprmat-0.1.26 → exprmat-0.1.27}/exprmat/utils.py +0 -0
  134. {exprmat-0.1.26 → exprmat-0.1.27}/license +0 -0
  135. {exprmat-0.1.26 → exprmat-0.1.27}/readme.md +0 -0
  136. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/Cargo.toml +0 -0
  137. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/license +0 -0
  138. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/readme +0 -0
  139. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/src/call_peaks.rs +0 -0
  140. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/src/embedding.rs +0 -0
  141. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/src/export.rs +0 -0
  142. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/src/knn.rs +0 -0
  143. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/src/lib.rs +0 -0
  144. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/src/motif.rs +0 -0
  145. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/src/network.rs +0 -0
  146. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/src/preprocessing.rs +0 -0
  147. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/src/utils/anndata.rs +0 -0
  148. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2/src/utils.rs +0 -0
  149. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/Cargo.toml +0 -0
  150. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/embedding.rs +0 -0
  151. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/export.rs +0 -0
  152. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/feature_count/counter.rs +0 -0
  153. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/feature_count/data_iter.rs +0 -0
  154. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/feature_count/matrix.rs +0 -0
  155. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/feature_count/mod.rs +0 -0
  156. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/genome.rs +0 -0
  157. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/lib.rs +0 -0
  158. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/motif.rs +0 -0
  159. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/network.rs +0 -0
  160. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/preprocessing/bam/flagstat.rs +0 -0
  161. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/preprocessing/bam/header.rs +0 -0
  162. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/preprocessing/bam/mark_duplicates.rs +0 -0
  163. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/preprocessing/bam.rs +0 -0
  164. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/preprocessing/import.rs +0 -0
  165. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/preprocessing/mod.rs +0 -0
  166. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/preprocessing/qc.rs +0 -0
  167. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/utils/knn.rs +0 -0
  168. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/utils/mod.rs +0 -0
  169. {exprmat-0.1.26 → exprmat-0.1.27}/snapatac2-core/src/utils/similarity.rs +0 -0
{exprmat-0.1.26 → exprmat-0.1.27}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: exprmat
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- Version: 0.1.26
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+ Version: 0.1.27
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  Classifier: Programming Language :: Rust
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  Classifier: Programming Language :: Python :: Implementation :: CPython
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  Classifier: Programming Language :: Python :: Implementation :: PyPy
{exprmat-0.1.26 → exprmat-0.1.27}/pyproject.toml RENAMED
@@ -7,6 +7,10 @@ features = ["pyo3/extension-module"]
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  python-source = "."
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  module-name = "exprmat.snapatac"
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  manifest-path = "snapatac2/Cargo.toml"
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+ exclude = [
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+ "exprmat/data/tools/**/*",
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+ "exprmat/data/tools/*"
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+ ]
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  [project]
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  name = "exprmat"
@@ -14,7 +18,7 @@ description = "exprmat: Routines for expression matrices"
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  readme = "readme.md"
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  license = {file = "license"}
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  requires-python = ">=3.9, <3.13"
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- version = "0.1.26"
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+ version = "0.1.27"
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  authors = [
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  {name = "Zheng Yang", email = "xornent@outlook.com"}
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  ]