User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
BSD-3-CLAUSE License
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Please refer to the release notes of all previous versions here
cell2cell.preprocessing.rnaseq.add_complexes_to_expression()
)Full Changelog: https://github.com/earmingol/cell2cell/compare/v0.7.3...v0.7.4
Published by earmingol 11 months ago
Please refer to the release notes of all previous versions here
docs
folder for readthedocs.org.cell2cell.plotting.pcoa_plot.pcoa_3dplot()
cell2cell.stats.permutation.compute_pvalue_from_dist()
cell2cell.analysis.cell2cell_pipelines.SingleCellInteractions
cell2cell.plotting.circular_plot.circos_plot()
Published by earmingol 11 months ago
Please refer to the release notes of all previous versions here
cell2cell.spatial
functions for enabling analyses considering spatial organization in spatial data.cell2cell.spatial.distances
and cell2cell.spatial.filtering
).cell2cell.spatial.neighborhoods.create_spatial_grid()
)cell2cell.spatial.neighborhoods.create_sliding_windows()
, cell2cell.spatial.neighborhoods.calculate_window_size()
,cell2cell.spatial.neighborhoods.add_sliding_window_info_to_adata()
)cell2cell.plotting.tensor_plot
Published by earmingol over 1 year ago
Please refer to the release notes of all previous versions here
cell2cell.external.gseapy.run_gsea()
Published by earmingol over 1 year ago
Please refer to the release notes of all previous versions here
interaction_elements
attribute from cell2cell.analysis.cell2cell_pipelines.SingleCellInteractions
cell2cell.analysis.cell2cell_pipelines.BulkInteractions
cell2cell.external.gseapy
cell2cell.analysis.cell2cell_pipelines.SingleCellInteractions.permute_cell_labels()
Published by earmingol over 1 year ago
Please refer to the release notes of all previous versions here
cell2cell.tensor.tensor.BaseTensor
and any otherBaseTensor.shape
, BaseTensor.write_file()
, BaseTensor.to_device()
.BaseTensor.tensor.shape
)cell2cell.analysis.tensor_pipelines.run_tensor_cell2cell_pipeline()
cell2cell.external.gseapy.run_gsea()
.Published by earmingol over 1 year ago
Please refer to the release notes of all previous versions here
cell2cell.datasets.gsea_data
and cell2cell.external.gseapy
.cell2cell.analysis.tensor_downstream.get_lr_by_cell_pairs()
.cell2cell.analysis.tensor_downstream.get_joint_loadings()
,dim1
and dim2
parameters.cm.ax_heatmap.set_xlabel()
& (cm.ax_heatmap.set_ylabel()
) using the dataframe axis namescell2cell.plotting.factor_plot.loading_clustermap()
Full Changelog: https://github.com/earmingol/cell2cell/compare/v0.6.4...v0.6.5
Published by earmingol over 1 year ago
Please refer to the release notes here.
cell2cell.io.read_data.load_tensor()
function to directly load a previouslyinteraction_tensor
variable generated with Tensor-cell2cell.cell2cell.datasets.anndata.balf_covid()
.cell2cell.io.directories
.cell2cell.io.read_data.load_tables_from_directory()
to load all tables or dataframes with the samesparsity_fraction()
and missing_fraction()
methods of cell2cell.tensor.tensor.BaseTensor
to returncell2cell.tensor.external_scores.dataframes_to_tensor()
.backend
when running cell2cell.analysis.tensor_pipelines.run_tensor_cell2cell_pipeline()
.cell2cell.tensor.external_scores.dataframes_to_tensor()
.dup_aggregation
.Full Changelog: https://github.com/earmingol/cell2cell/commits/v0.6.4