sclab 0.3.2__py3-none-any.whl → 0.3.4__py3-none-any.whl

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Files changed (27) hide show
  1. sclab/__init__.py +1 -1
  2. sclab/examples/processor_steps/_integration.py +4 -1
  3. sclab/examples/processor_steps/_preprocess.py +34 -18
  4. sclab/preprocess/__init__.py +8 -1
  5. sclab/preprocess/_cca.py +26 -4
  6. sclab/preprocess/_cca_integrate.py +4 -4
  7. sclab/preprocess/_normalize_weighted.py +5 -1
  8. sclab/preprocess/_pca.py +51 -0
  9. sclab/preprocess/_preprocess.py +155 -0
  10. sclab/preprocess/_qc.py +38 -0
  11. sclab/preprocess/_rpca.py +116 -0
  12. sclab/preprocess/_transfer_metadata.py +90 -31
  13. sclab/tools/cellflow/pseudotime/_pseudotime.py +5 -1
  14. sclab/tools/cellflow/utils/periodic_genes.py +106 -0
  15. sclab/tools/differential_expression/__init__.py +2 -0
  16. sclab/tools/differential_expression/_pseudobulk_edger.py +28 -23
  17. sclab/tools/differential_expression/_pseudobulk_helpers.py +15 -2
  18. sclab/tools/differential_expression/_pseudobulk_limma.py +257 -0
  19. sclab/tools/embedding/__init__.py +0 -0
  20. sclab/tools/imputation/__init__.py +0 -0
  21. sclab/tools/imputation/_alra.py +135 -0
  22. sclab/tools/utils/__init__.py +5 -0
  23. sclab/tools/utils/_aggregate_and_filter.py +290 -0
  24. {sclab-0.3.2.dist-info → sclab-0.3.4.dist-info}/METADATA +6 -5
  25. {sclab-0.3.2.dist-info → sclab-0.3.4.dist-info}/RECORD +27 -16
  26. {sclab-0.3.2.dist-info → sclab-0.3.4.dist-info}/WHEEL +0 -0
  27. {sclab-0.3.2.dist-info → sclab-0.3.4.dist-info}/licenses/LICENSE +0 -0
{sclab-0.3.2.dist-info → sclab-0.3.4.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: sclab
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- Version: 0.3.2
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+ Version: 0.3.4
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  Summary: sclab
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  Author-email: Argenis Arriojas <ArriojasMaldonado001@umb.edu>
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  Requires-Python: >=3.10,<3.13
@@ -22,6 +22,7 @@ Requires-Dist: plotly<6.0
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  Requires-Dist: requests
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  Requires-Dist: ripser>=0.6.12
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  Requires-Dist: scikit-learn
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+ Requires-Dist: scipy<1.16
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  Requires-Dist: svgpathtools
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  Requires-Dist: tqdm
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  Requires-Dist: jupyterlab>=4.3.6 ; extra == "jupyter"
@@ -65,7 +66,6 @@ Open a Jupyter Notebook and run the following:
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  ```python
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  from IPython.display import display
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  from sclab import SCLabDashboard
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- from sclab.examples.processor_steps import QC, Preprocess, PCA, Neighbors, UMAP, Cluster
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  import scanpy as sc
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  # Load your data
@@ -73,8 +73,6 @@ adata = sc.read_10x_h5("your_data.h5")
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  # Create dashboard
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  dashboard = SCLabDashboard(adata, name="My Analysis")
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- # Add desired processing steps to the interface
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- dashboard.pr.add_steps({"Processing": [QC, Preprocess, PCA, Neighbors, UMAP, Cluster]})
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  # Display dashboard
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  display(dashboard)
@@ -84,8 +82,10 @@ display(dashboard)
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  # dashboard.pl # Plotter
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  # dashboard.pr # Processor
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- # the resulting AnnData object is found within the dataset object:
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+ # the active AnnData object is found within the dataset object:
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  # dashboard.ds.adata
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+
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+ # by default, the dashboard will update the loaded AnnData object in-place
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  ```
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  ## Components
@@ -94,6 +94,7 @@ display(dashboard)
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  The main interface that integrates all components with a tabbed layout:
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  - Main graph for visualizations
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+ - Results panel
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  - Observations table
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  - Genes table
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  - Event logs
{sclab-0.3.2.dist-info → sclab-0.3.4.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
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- sclab/__init__.py,sha256=3ni3MpADkty43xRMRFsxvB_jIrmOjxyMKFGhHsYx8Ho,132
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+ sclab/__init__.py,sha256=h0wOZ8nYaO0JUqkCgv5svKUlfN_a5SH05oC5WQ-ccfs,132
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  sclab/_io.py,sha256=5ISxIPbE233UiOt3QEs9fkLO8DLLEe5HrMnZoR-KLYE,2662
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  sclab/_methods_registry.py,sha256=RcffyRuuLzHqsnAdbBL4W1GmZx80d9AxdGjUnx1mbNg,1704
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  sclab/_sclab.py,sha256=m9y2EgDxFO5JHZAZIK1098bHdrZxaeWfBZNyGQkFCdA,9143
@@ -25,10 +25,10 @@ sclab/examples/processor_steps/_cluster.py,sha256=olbri3HWPBU8p__r9kP9tgWaJoUJ2b
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  sclab/examples/processor_steps/_differential_expression.py,sha256=bIR334XDWWkfL7EHgysFsx6PCwdvMuh23J-jnUuptJA,11617
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  sclab/examples/processor_steps/_doublet_detection.py,sha256=eFQtRsdvBWJ_v3HH08v-KbjYius-fj1pg1HBm0mjADg,2114
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  sclab/examples/processor_steps/_gene_expression.py,sha256=io_U53TQ3bpclGZ7xjuQHws4Lei5_nMpWTKbvD2zqs0,4216
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- sclab/examples/processor_steps/_integration.py,sha256=40nIM19VnBALMQXYO9XpYczH7gEcpIUb-DLdYraxzxs,3444
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+ sclab/examples/processor_steps/_integration.py,sha256=TXk-7K6FXPB8NooSjSG-NDBsYGZW_EMYMfptGqtRXww,3506
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  sclab/examples/processor_steps/_neighbors.py,sha256=jGpoPtlN8nlcsOqUOiqTPQgGzbpToLAVR1By2SHBo5U,2949
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  sclab/examples/processor_steps/_pca.py,sha256=kULbPPTAMqAgECyycmpf5dpU-FYPJSLbTO-UEkOb5mo,4798
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- sclab/examples/processor_steps/_preprocess.py,sha256=kKqOQWyBC3BFLYVsCWRPwaXHeuWG1s69puvwhDQK5Eg,6809
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+ sclab/examples/processor_steps/_preprocess.py,sha256=ANjiYBHO1xhHJQ52o8Sl_wje6xQokKeYQWYmkYEad08,7527
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  sclab/examples/processor_steps/_qc.py,sha256=3e5TTGPNWbGPJBX0Sx18np8qcrgPznUuJJ-DwCrRZ0U,3684
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  sclab/examples/processor_steps/_umap.py,sha256=Mzxj4LiZfh3WT5lS_BO_lTleC5jMoUm5_km_gvzU_I8,1402
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  sclab/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -36,15 +36,19 @@ sclab/gui/components/__init__.py,sha256=X0-cGJmII76qpWHEBe49miS2gPw3esMAwp61z23w
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  sclab/gui/components/_guided_pseudotime.py,sha256=sxI0jmZxD4fxV9CsTJONhINWzIL--YF3nDg0nku2yp8,17670
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  sclab/gui/components/_transfer_metadata.py,sha256=o9t9bQ7tr3G2-vFptUu1IiMxGhvMq-QJb_lF7AsDhQQ,6236
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  sclab/methods/__init__.py,sha256=d_n5SCyzwMEBZttXwnhgkx2FnD7AxhAK9yBre6Rynfk,1215
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- sclab/preprocess/__init__.py,sha256=zGt-TIDRx3qoKDpFxqnZ9yf2AfP4HBy8ZZSFLx-rGj0,547
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- sclab/preprocess/_cca.py,sha256=etDk1s3rKX-r0nkRuUaLTJ7NyalauCpWXyKRq1_EwTc,4400
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- sclab/preprocess/_cca_integrate.py,sha256=14Tu6TyH7wfZYAM2EsII1R92PTxfhaYbGx4bLWlMLP0,2706
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+ sclab/preprocess/__init__.py,sha256=MM6A5SKboFSwaOnykYJmfkBrT2dXyAJq4TR5uYyxHh8,710
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+ sclab/preprocess/_cca.py,sha256=77J_v5IJnHsLJnnhYmKtq2e_mJwQlsdGgB6lSIftf4Q,5080
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+ sclab/preprocess/_cca_integrate.py,sha256=eIvEdUon7OkNY-kbEqRJeuIaj_m6wk72PcRFow1kH9g,2710
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  sclab/preprocess/_filter_obs.py,sha256=uYlcljuaq85G44Si8oxrNRcCCX2nFRdT3RN3ArqnwaY,1166
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  sclab/preprocess/_harmony.py,sha256=wpFQXpr13BvljT04I_Rw5JdBvhzvAuinkrRs152CfvQ,13747
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  sclab/preprocess/_harmony_integrate.py,sha256=cKN_MyYq9FtwgQZyhgxiFNTZl36YuKLQdEoc7ky-ea4,1737
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- sclab/preprocess/_normalize_weighted.py,sha256=h86rQakNoXoRKOepAEoBbBtHV_F-VMG2-uW_LcaSdWs,1587
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+ sclab/preprocess/_normalize_weighted.py,sha256=Y_Tk3Dvv-Dd4s6D7JkAsuPLCCucrgmnAZBSrDssNFMU,1696
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+ sclab/preprocess/_pca.py,sha256=fFR03B1_V7CLcZXSn5Ek9HqG_zSLwVK7DUf8XgPZIoQ,1606
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+ sclab/preprocess/_preprocess.py,sha256=-Ve6HLbyzuqxwoUW1rd1JGb_ZWRwo4KV6ri7l-hvVjY,5200
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+ sclab/preprocess/_qc.py,sha256=CblkoK0CB2bkjgLuGAxcyYb89ZjhhS5NEhO4RgIQI4I,1159
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+ sclab/preprocess/_rpca.py,sha256=eLXVTgaZOl7uo7o5bDsKslQX7DV0Gjk9qbf23iNT1Vg,3146
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  sclab/preprocess/_subset.py,sha256=8Vc5jty8WzIf8NZ1mleqNJLAp5CRWvEXGVevlT6ekNk,7066
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- sclab/preprocess/_transfer_metadata.py,sha256=HA11JHHpq4ueFTeXlU4K3kHDDUzcUjyvfxpzdPBRNTo,4307
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+ sclab/preprocess/_transfer_metadata.py,sha256=PwFL99paaqnmZeZIIAGvncYlhbr27solyMI5_nC3Ipw,5823
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  sclab/preprocess/_transform.py,sha256=n2xHJR3T-rRxZneCFH2oMw9RaQcGGBfHpOu1-YP1c1E,2312
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  sclab/preprocess/_utils.py,sha256=dLeS_fIvQGZZfesEtbJKtnPmqjqy3fmyTC4GewRD3Fc,3078
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  sclab/scanpy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -60,23 +64,30 @@ sclab/tools/cellflow/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hS
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  sclab/tools/cellflow/density_dynamics/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  sclab/tools/cellflow/density_dynamics/_density_dynamics.py,sha256=xzmeIAHLV5xIVERpWMClZViDpJcge_dPsx6GWI0j0R8,11038
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  sclab/tools/cellflow/pseudotime/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- sclab/tools/cellflow/pseudotime/_pseudotime.py,sha256=RiwbOduu0InNdh2Rp8DUXG6-r5wL_vVUGTyTkwnYhTY,9842
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+ sclab/tools/cellflow/pseudotime/_pseudotime.py,sha256=Wud0ooPtNmManLsNiUgMHtx5TzIHs6vIXsWTu2M1hE0,9940
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  sclab/tools/cellflow/pseudotime/timeseries.py,sha256=ZuMAm9LOKksJy2FzsQg3rdYKtLm1G0rbgO6dOdQuIV0,6326
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  sclab/tools/cellflow/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  sclab/tools/cellflow/utils/density_nd.py,sha256=wwYoXOcF2CRxOArW_CQxJjWDE90wiui4NO7EIBG2RGM,6648
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  sclab/tools/cellflow/utils/interpolate.py,sha256=HnpYEBdc4KSPC4QYOglJ2MpipLx3a5ENJQ8uhMnuwRc,9755
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+ sclab/tools/cellflow/utils/periodic_genes.py,sha256=HSrMcBbs7nQJ0EJGzmPKkFe63AL8ZQFxZ2z9VCsy8mw,3467
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  sclab/tools/cellflow/utils/smoothen.py,sha256=yg2_zBrYKGRmXZY8C3pKmX3xGm0GGMI365IKqhgCmP0,3738
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  sclab/tools/cellflow/utils/times.py,sha256=lV5ZRjCdBaYELGJ1pGdEBeA0w-WD77lOzPC6R7_kUxo,1811
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- sclab/tools/differential_expression/__init__.py,sha256=KKaDzeGGgE1LxnC5aBcPQYcVX_e2h8qAbfMPQVvYlSA,87
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- sclab/tools/differential_expression/_pseudobulk_edger.py,sha256=WWqKEA8I1I_YsgjafeznX3tyZoXyu0HV13QkxiYGFgQ,10538
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- sclab/tools/differential_expression/_pseudobulk_helpers.py,sha256=raQ0DBBrmrxBbGTKhOyZpZLmeJRX_tWcn3_mzuQctkw,8424
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+ sclab/tools/differential_expression/__init__.py,sha256=xdmdaCYdJDxiY5g4o8mQHCk4Z6gUZv92gvLiF81nA-M,159
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+ sclab/tools/differential_expression/_pseudobulk_edger.py,sha256=PUnVgpWDQMoJq7KWLE6OWODh5ZUTXPz1FNVR7h_CXGU,10618
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+ sclab/tools/differential_expression/_pseudobulk_helpers.py,sha256=5o4VAJgY1X-FlMYbYGMm1SasqpLLm7umaR-ZRH69xjg,8908
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+ sclab/tools/differential_expression/_pseudobulk_limma.py,sha256=dOjVSeV_-Pycj9vzOwhHNF2o5eduMHcDJGIbu3wMjdg,8395
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  sclab/tools/doublet_detection/__init__.py,sha256=zWyAPScrHVRaBqWaizVsm2H3oi6yr0OQ5gF-fGY2ZrA,63
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  sclab/tools/doublet_detection/_scrublet.py,sha256=koi6MRUS1lWVvdpeNbzpR8njqVFrWEuWoKNMFXQLFec,1953
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+ sclab/tools/embedding/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ sclab/tools/imputation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ sclab/tools/imputation/_alra.py,sha256=tbj8ic-PXy94QJWGs4nG2KxveP7SjuQ64yZHv5hkuXQ,3460
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  sclab/tools/labeling/__init__.py,sha256=o-FJWonGNr2h_pB0o3YfnGl_y1kKU06_rYLmTt8ktlQ,57
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  sclab/tools/labeling/sctype.py,sha256=jCsCFnqUgb_s1nTSK-N_5pEL_ZvZw-zUo12fUy9RLfs,8164
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+ sclab/tools/utils/__init__.py,sha256=r1NZUuhw9bQMSr93DzdKEMpvfz2L9Axz99xT5dSKBbE,99
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+ sclab/tools/utils/_aggregate_and_filter.py,sha256=5o4VAJgY1X-FlMYbYGMm1SasqpLLm7umaR-ZRH69xjg,8908
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  sclab/utils/__init__.py,sha256=Py3dPN9ptMs6D-f7IGYisoxOS2YuX0O1oyw75nci3Os,72
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  sclab/utils/_write_excel.py,sha256=DBZg9Kx7Ex6VqFrZFDZbSgvzMtu84iEwKo4nI3I2AT0,17017
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- sclab-0.3.2.dist-info/licenses/LICENSE,sha256=LO7qldZoHIo9hc-HMBqclBh5800kZ9US9xTbLAQdHpg,1523
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- sclab-0.3.2.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
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- sclab-0.3.2.dist-info/METADATA,sha256=YOX9WvDuWL1ew3JOIaAwY6MvpCHCEHxOdTc6dTCp9jM,4437
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- sclab-0.3.2.dist-info/RECORD,,
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+ sclab-0.3.4.dist-info/licenses/LICENSE,sha256=LO7qldZoHIo9hc-HMBqclBh5800kZ9US9xTbLAQdHpg,1523
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+ sclab-0.3.4.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
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+ sclab-0.3.4.dist-info/METADATA,sha256=vwZbQeG7-UPeikCDq6Op0fXmx-67dztOWd3WY8C0UjM,4327
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+ sclab-0.3.4.dist-info/RECORD,,
{sclab-0.3.2.dist-info → sclab-0.3.4.dist-info}/WHEEL RENAMED
File without changes