exprmat 0.1.19__tar.gz → 0.1.23__tar.gz

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Files changed (258) hide show
  1. exprmat-0.1.23/Cargo.lock +4131 -0
  2. exprmat-0.1.23/Cargo.toml +6 -0
  3. exprmat-0.1.23/PKG-INFO +88 -0
  4. exprmat-0.1.23/exprmat/__init__.py +64 -0
  5. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/ansi.py +0 -1
  6. exprmat-0.1.23/exprmat/clustering/cnmf.py +495 -0
  7. exprmat-0.1.23/exprmat/clustering/nmf.py +31 -0
  8. exprmat-0.1.23/exprmat/clustering/seriation.py +64 -0
  9. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/configuration.py +1 -0
  10. exprmat-0.1.23/exprmat/data/cistarget.py +697 -0
  11. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/finders.py +1 -1
  12. exprmat-0.1.23/exprmat/data/hsa/genesets/curated/macrophage-atlas.gmt +54 -0
  13. exprmat-0.1.23/exprmat/data/hsa/genesets/curated/t-cell-atlas.gmt +41 -0
  14. exprmat-0.1.23/exprmat/data/hsa/genesets/curated/t-cell-development.gmt +8 -0
  15. exprmat-0.1.23/exprmat/data/io.py +8 -0
  16. exprmat-0.1.23/exprmat/data/mmu/genesets/curated/cgas-sting.gmt +1 -0
  17. exprmat-0.1.23/exprmat/data/mmu/genesets/curated/cgas-targets.gmt +1 -0
  18. exprmat-0.1.23/exprmat/data/mmu/genesets/curated/nfkb-downregulated.gmt +1 -0
  19. exprmat-0.1.23/exprmat/data/mmu/genesets/curated/nfkb-targets.gmt +1 -0
  20. exprmat-0.1.23/exprmat/data/mmu/genesets/curated/nfkb-upregulated.gmt +1 -0
  21. exprmat-0.1.23/exprmat/data/mmu/genesets/curated/nfkb.gmt +1 -0
  22. exprmat-0.1.23/exprmat/data/signature.py +325 -0
  23. exprmat-0.1.23/exprmat/data/tf.py +36 -0
  24. exprmat-0.1.23/exprmat/descriptive/aucell.py +200 -0
  25. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/descriptive/gse.py +42 -17
  26. exprmat-0.1.23/exprmat/descriptive/recovery.py +369 -0
  27. exprmat-0.1.23/exprmat/grn/__init__.py +100 -0
  28. exprmat-0.1.23/exprmat/grn/infergrn.py +92 -0
  29. exprmat-0.1.23/exprmat/grn/modules.py +392 -0
  30. exprmat-0.1.23/exprmat/grn/prune.py +491 -0
  31. exprmat-0.1.23/exprmat/grn/regressors.py +364 -0
  32. exprmat-0.1.23/exprmat/grn/utils.py +154 -0
  33. exprmat-0.1.23/exprmat/plotting/cnmf.py +66 -0
  34. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/plotting/expression.py +9 -6
  35. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/plotting/gse.py +12 -6
  36. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/preprocessing/integrate.py +22 -0
  37. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/preprocessing/linear.py +5 -5
  38. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/reader/experiment.py +169 -4
  39. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/reader/matcher.py +38 -6
  40. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/reduction/plot.py +12 -2
  41. exprmat-0.1.23/exprmat/trajectory/pcurve.py +210 -0
  42. exprmat-0.1.23/exprmat/transfer/__init__.py +0 -0
  43. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/utils.py +59 -1
  44. exprmat-0.1.23/license +0 -0
  45. exprmat-0.1.23/pyproject.toml +84 -0
  46. exprmat-0.1.23/readme.md +26 -0
  47. exprmat-0.1.23/snapatac2/Cargo.toml +50 -0
  48. exprmat-0.1.23/snapatac2/license +20 -0
  49. exprmat-0.1.23/snapatac2/readme +4 -0
  50. exprmat-0.1.23/snapatac2/src/call_peaks.rs +603 -0
  51. exprmat-0.1.23/snapatac2/src/embedding.rs +463 -0
  52. exprmat-0.1.23/snapatac2/src/export.rs +95 -0
  53. exprmat-0.1.23/snapatac2/src/knn.rs +28 -0
  54. exprmat-0.1.23/snapatac2/src/lib.rs +83 -0
  55. exprmat-0.1.23/snapatac2/src/motif.rs +165 -0
  56. exprmat-0.1.23/snapatac2/src/network.rs +40 -0
  57. exprmat-0.1.23/snapatac2/src/preprocessing.rs +564 -0
  58. exprmat-0.1.23/snapatac2/src/utils/anndata.rs +268 -0
  59. exprmat-0.1.23/snapatac2/src/utils.rs +414 -0
  60. exprmat-0.1.23/snapatac2-core/Cargo.toml +37 -0
  61. exprmat-0.1.23/snapatac2-core/src/embedding.rs +22 -0
  62. exprmat-0.1.23/snapatac2-core/src/export.rs +701 -0
  63. exprmat-0.1.23/snapatac2-core/src/feature_count/counter.rs +289 -0
  64. exprmat-0.1.23/snapatac2-core/src/feature_count/data_iter.rs +1005 -0
  65. exprmat-0.1.23/snapatac2-core/src/feature_count/matrix.rs +273 -0
  66. exprmat-0.1.23/snapatac2-core/src/feature_count/mod.rs +128 -0
  67. exprmat-0.1.23/snapatac2-core/src/genome.rs +637 -0
  68. exprmat-0.1.23/snapatac2-core/src/lib.rs +11 -0
  69. exprmat-0.1.23/snapatac2-core/src/motif.rs +322 -0
  70. exprmat-0.1.23/snapatac2-core/src/network.rs +76 -0
  71. exprmat-0.1.23/snapatac2-core/src/preprocessing/bam/flagstat.rs +325 -0
  72. exprmat-0.1.23/snapatac2-core/src/preprocessing/bam/header.rs +202 -0
  73. exprmat-0.1.23/snapatac2-core/src/preprocessing/bam/mark_duplicates.rs +351 -0
  74. exprmat-0.1.23/snapatac2-core/src/preprocessing/bam.rs +192 -0
  75. exprmat-0.1.23/snapatac2-core/src/preprocessing/import.rs +411 -0
  76. exprmat-0.1.23/snapatac2-core/src/preprocessing/mod.rs +11 -0
  77. exprmat-0.1.23/snapatac2-core/src/preprocessing/qc.rs +631 -0
  78. exprmat-0.1.23/snapatac2-core/src/utils/knn.rs +79 -0
  79. exprmat-0.1.23/snapatac2-core/src/utils/mod.rs +153 -0
  80. exprmat-0.1.23/snapatac2-core/src/utils/similarity.rs +410 -0
  81. exprmat-0.1.19/PKG-INFO +0 -42
  82. exprmat-0.1.19/exprmat/__init__.py +0 -33
  83. exprmat-0.1.19/exprmat/data/hsa/mapping-ensembl.pkl +0 -0
  84. exprmat-0.1.19/exprmat/data/hsa/mapping-name.pkl +0 -0
  85. exprmat-0.1.19/exprmat/data/mmu/mapping-ensembl.pkl +0 -0
  86. exprmat-0.1.19/exprmat/data/mmu/mapping-name.pkl +0 -0
  87. exprmat-0.1.19/exprmat.egg-info/PKG-INFO +0 -42
  88. exprmat-0.1.19/exprmat.egg-info/SOURCES.txt +0 -188
  89. exprmat-0.1.19/exprmat.egg-info/dependency_links.txt +0 -1
  90. exprmat-0.1.19/exprmat.egg-info/not-zip-safe +0 -1
  91. exprmat-0.1.19/exprmat.egg-info/requires.txt +0 -28
  92. exprmat-0.1.19/exprmat.egg-info/top_level.txt +0 -1
  93. exprmat-0.1.19/setup.cfg +0 -4
  94. exprmat-0.1.19/setup.py +0 -57
  95. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/clustering/__init__.py +0 -0
  96. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/clustering/leiden.py +0 -0
  97. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/clustering/rogue.py +0 -0
  98. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/clustering/spectral.py +0 -0
  99. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/clustering/utils.py +0 -0
  100. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/cnv/__init__.py +0 -0
  101. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/cnv/cnvscore.py +0 -0
  102. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/cnv/infercnv.py +0 -0
  103. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/__init__.py +0 -0
  104. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/delim.py +0 -0
  105. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/geneset.py +0 -0
  106. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/gff.py +0 -0
  107. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/entrez.tsv.gz +0 -0
  108. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/all.gmt +0 -0
  109. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/bp.gmt +0 -0
  110. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/cancer-modules.gmt +0 -0
  111. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/cancer-neighborhoods.gmt +0 -0
  112. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/cancer.gmt +0 -0
  113. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/cc.gmt +0 -0
  114. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/chemical-perturb.gmt +0 -0
  115. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/hallmark.gmt +0 -0
  116. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/human-phenotype-ontology.gmt +0 -0
  117. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/immune-perturb.gmt +0 -0
  118. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/kegg.gmt +0 -0
  119. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/mf.gmt +0 -0
  120. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/microrna.gmt +0 -0
  121. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/oncogenic.gmt +0 -0
  122. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/pathways.gmt +0 -0
  123. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/positional.gmt +0 -0
  124. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/single-cell.gmt +0 -0
  125. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/transcript-factors.gmt +0 -0
  126. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genesets/vaccine.gmt +0 -0
  127. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/genome.tsv.gz +0 -0
  128. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/baccin2019 +0 -0
  129. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/cellcall +0 -0
  130. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/cellchatdb +0 -0
  131. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/cellinker +0 -0
  132. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/cellphonedb +0 -0
  133. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/celltalkdb +0 -0
  134. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/connectomedb2020 +0 -0
  135. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/consensus +0 -0
  136. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/embrace +0 -0
  137. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/guide2pharma +0 -0
  138. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/hpmr +0 -0
  139. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/icellnet +0 -0
  140. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/italk +0 -0
  141. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/kirouac2010 +0 -0
  142. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/lrdb +0 -0
  143. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/lr/ramilowski2015 +0 -0
  144. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/aca.tsv.gz +0 -0
  145. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/bta.tsv.gz +0 -0
  146. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/cel.tsv.gz +0 -0
  147. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/clu.tsv.gz +0 -0
  148. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/dme.tsv.gz +0 -0
  149. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/dre.tsv.gz +0 -0
  150. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/eca.tsv.gz +0 -0
  151. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/fca.tsv.gz +0 -0
  152. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/gga.tsv.gz +0 -0
  153. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/mdo.tsv.gz +0 -0
  154. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/mmu.tsv.gz +0 -0
  155. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/mmul.gz +0 -0
  156. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/oan.tsv.gz +0 -0
  157. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/ptr.tsv.gz +0 -0
  158. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/rno.tsv.gz +0 -0
  159. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/sce.tsv.gz +0 -0
  160. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/spo.tsv.gz +0 -0
  161. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/ssc.tsv.gz +0 -0
  162. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/orthologs/xla.tsv.gz +0 -0
  163. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/hsa/taxa +0 -0
  164. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/lr.py +0 -0
  165. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/entrez.tsv.gz +0 -0
  166. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/all.gmt +0 -0
  167. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/azimuth.gmt +0 -0
  168. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/biocarta.gmt +0 -0
  169. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/bp.gmt +0 -0
  170. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/cc.gmt +0 -0
  171. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/chemical-perturb.gmt +0 -0
  172. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/hallmark.gmt +0 -0
  173. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/kegg.gmt +0 -0
  174. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/m2.gmt +0 -0
  175. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/markers.gmt +0 -0
  176. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/mf.gmt +0 -0
  177. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/microrna.gmt +0 -0
  178. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/mpt.gmt +0 -0
  179. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/positional.gmt +0 -0
  180. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/reactome.gmt +0 -0
  181. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/transcript-factors.gmt +0 -0
  182. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genesets/wikipathway.gmt +0 -0
  183. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/genome.tsv.gz +0 -0
  184. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/lr/consensus +0 -0
  185. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/mmu/taxa +0 -0
  186. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/presets.py +0 -0
  187. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/private.py +0 -0
  188. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/data/ranges.py +0 -0
  189. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/descriptive/__init__.py +0 -0
  190. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/descriptive/aggregate.py +0 -0
  191. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/descriptive/de.py +0 -0
  192. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/descriptive/kde.py +0 -0
  193. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/descriptive/summary.py +0 -0
  194. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/descriptive/tcr.py +0 -0
  195. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/dynamics/__init__.py +0 -0
  196. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/dynamics/generank.py +0 -0
  197. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/dynamics/linreg.py +0 -0
  198. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/dynamics/moments.py +0 -0
  199. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/dynamics/optimization.py +0 -0
  200. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/dynamics/parallel.py +0 -0
  201. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/dynamics/preprocess.py +0 -0
  202. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/dynamics/pseudotime.py +0 -0
  203. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/dynamics/transition.py +0 -0
  204. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/dynamics/utils.py +0 -0
  205. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/dynamics/velocity.py +0 -0
  206. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/lr/__init__.py +0 -0
  207. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/lr/aggregate.py +0 -0
  208. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/lr/method.py +0 -0
  209. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/lr/methods/__init__.py +0 -0
  210. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/lr/methods/cellchat.py +0 -0
  211. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/lr/methods/cellphonedb.py +0 -0
  212. {exprmat-0.1.19 → exprmat-0.1.23}/exprmat/lr/methods/connectome.py +0 -0
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