spatialsnake 0.0.1__py3-none-any.whl

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 (89) hide show
  1. spatialsnake/__init__.py +0 -0
  2. spatialsnake/command_line.py +715 -0
  3. spatialsnake/config.yaml +69 -0
  4. spatialsnake/workflow/Snakefile +589 -0
  5. spatialsnake/workflow/envs/advance_analysis.yaml +83 -0
  6. spatialsnake/workflow/envs/annotation.yaml +47 -0
  7. spatialsnake/workflow/envs/annotation_help.yaml +20 -0
  8. spatialsnake/workflow/envs/clustering.yaml +24 -0
  9. spatialsnake/workflow/envs/compare_stage.yaml +43 -0
  10. spatialsnake/workflow/envs/integrate.yaml +68 -0
  11. spatialsnake/workflow/envs/merge.yaml +12 -0
  12. spatialsnake/workflow/envs/preprocess.yaml +23 -0
  13. spatialsnake/workflow/envs/reclustering.yaml +12 -0
  14. spatialsnake/workflow/envs/splitting.yaml +21 -0
  15. spatialsnake/workflow/envs/transform.yaml +12 -0
  16. spatialsnake/workflow/function/export_cluster_csv.py +84 -0
  17. spatialsnake/workflow/function/get_sample.py +343 -0
  18. spatialsnake/workflow/function/legacy_anndata.py +546 -0
  19. spatialsnake/workflow/function/merfish_utils.py +173 -0
  20. spatialsnake/workflow/function/merge.py +252 -0
  21. spatialsnake/workflow/function/pca_choosing.py +35 -0
  22. spatialsnake/workflow/function/plot.py +484 -0
  23. spatialsnake/workflow/function/splitting.py +280 -0
  24. spatialsnake/workflow/function/stereoseq_selection.py +144 -0
  25. spatialsnake/workflow/function/stereoseq_spec.py +42 -0
  26. spatialsnake/workflow/function/stereoseq_v8.py +463 -0
  27. spatialsnake/workflow/function/transform.py +189 -0
  28. spatialsnake/workflow/get_sample.smk +187 -0
  29. spatialsnake/workflow/rules/RCTD.smk +51 -0
  30. spatialsnake/workflow/rules/advance_analysis.smk +24 -0
  31. spatialsnake/workflow/rules/annotation_help.smk +106 -0
  32. spatialsnake/workflow/rules/cell2Location_run.smk +71 -0
  33. spatialsnake/workflow/rules/cellPhoneDB.smk +97 -0
  34. spatialsnake/workflow/rules/cluster.smk +66 -0
  35. spatialsnake/workflow/rules/compare_LR.smk +52 -0
  36. spatialsnake/workflow/rules/compare_gene.smk +50 -0
  37. spatialsnake/workflow/rules/enrich.smk +36 -0
  38. spatialsnake/workflow/rules/integrate.smk +125 -0
  39. spatialsnake/workflow/rules/mannul.smk +58 -0
  40. spatialsnake/workflow/rules/merge.smk +43 -0
  41. spatialsnake/workflow/rules/preprocess.smk +81 -0
  42. spatialsnake/workflow/rules/py_senic.smk +87 -0
  43. spatialsnake/workflow/rules/reannotation.smk +48 -0
  44. spatialsnake/workflow/rules/reclustering.smk +34 -0
  45. spatialsnake/workflow/rules/run_banksy.smk +29 -0
  46. spatialsnake/workflow/rules/run_cellcharter.smk +39 -0
  47. spatialsnake/workflow/rules/run_cellchat.smk +48 -0
  48. spatialsnake/workflow/rules/run_liana.smk +56 -0
  49. spatialsnake/workflow/rules/run_slice.smk +22 -0
  50. spatialsnake/workflow/scripts/Cellchat.R +550 -0
  51. spatialsnake/workflow/scripts/DEG_visualize.R +110 -0
  52. spatialsnake/workflow/scripts/DEseq2.py +174 -0
  53. spatialsnake/workflow/scripts/Multi-cellchat.py +0 -0
  54. spatialsnake/workflow/scripts/QC.py +176 -0
  55. spatialsnake/workflow/scripts/RCTD.R +581 -0
  56. spatialsnake/workflow/scripts/RCTD_visualize.py +255 -0
  57. spatialsnake/workflow/scripts/advance_analyze.py +230 -0
  58. spatialsnake/workflow/scripts/cell2Location.py +389 -0
  59. spatialsnake/workflow/scripts/cell2locate_visualize.py +344 -0
  60. spatialsnake/workflow/scripts/cellchat_compare.R +353 -0
  61. spatialsnake/workflow/scripts/cellphoneDB.py +189 -0
  62. spatialsnake/workflow/scripts/cellphoneDB_visualize.py +186 -0
  63. spatialsnake/workflow/scripts/cluster_visualize.py +275 -0
  64. spatialsnake/workflow/scripts/clustering.py +195 -0
  65. spatialsnake/workflow/scripts/diffent_analysis.R +768 -0
  66. spatialsnake/workflow/scripts/enrichment.R +729 -0
  67. spatialsnake/workflow/scripts/h5ad_to_seurat.R +62 -0
  68. spatialsnake/workflow/scripts/install_packages.R +91 -0
  69. spatialsnake/workflow/scripts/mannul_annotation.py +294 -0
  70. spatialsnake/workflow/scripts/preprocessing.py +261 -0
  71. spatialsnake/workflow/scripts/pyscenic_numpy_compat.py +73 -0
  72. spatialsnake/workflow/scripts/pysenic.py +90 -0
  73. spatialsnake/workflow/scripts/pysenic_visualize.py +221 -0
  74. spatialsnake/workflow/scripts/reannotation.py +318 -0
  75. spatialsnake/workflow/scripts/reclustering.py +157 -0
  76. spatialsnake/workflow/scripts/run_banksy.py +270 -0
  77. spatialsnake/workflow/scripts/run_cellcharter.py +373 -0
  78. spatialsnake/workflow/scripts/run_liana.py +241 -0
  79. spatialsnake/workflow/scripts/seurat_to_h5ad.R +21 -0
  80. spatialsnake/workflow/scripts/slice_out.py +0 -0
  81. spatialsnake/workflow/scripts/spatial_in.py +608 -0
  82. spatialsnake/workflow/scripts/spatial_in_multiple.py +439 -0
  83. spatialsnake/workflow/scripts/subset.py +25 -0
  84. spatialsnake-0.0.1.dist-info/METADATA +289 -0
  85. spatialsnake-0.0.1.dist-info/RECORD +89 -0
  86. spatialsnake-0.0.1.dist-info/WHEEL +5 -0
  87. spatialsnake-0.0.1.dist-info/entry_points.txt +2 -0
  88. spatialsnake-0.0.1.dist-info/licenses/LICENSE +9 -0
  89. spatialsnake-0.0.1.dist-info/top_level.txt +1 -0
spatialsnake/__init__.py ADDED
File without changes