Harmonization Tools

This module encompasses a suite of tools designed for the harmonization of gene expression data derived from different sequencing technologies. Specifically, it provides functionality to standardize short-read gene expression matrices with long-read transcript matrices. The harmonization process ensures that datasets from disparate sources can be directly compared and analyzed together, facilitating integrative studies and enhancing the robustness of biological insights. The tools within this notebook are part of a larger ecosystem aimed at streamlining the analysis of transcriptomic data.

Harmonize two datasets by extracting a subset from one dataset containing only the cells that are also present in the other dataset, and by ensuring that the metadata and gene expression measurements are compatible for comparative analysis. This process facilitates the integration of datasets from different sequencing technologies or experimental conditions, allowing for robust downstream analyses such as differential expression, clustering, and trajectory inference.

source

subset_common_cells

 subset_common_cells (dataset1:anndata._core.anndata.AnnData,
                      dataset2:anndata._core.anndata.AnnData)

Subset dataset1 to only include cells that are also present in dataset2.

	Type	Details
dataset1	AnnData	First dataset to be subsetted.
dataset2	AnnData	Second dataset to compare with.
Returns	AnnData	Subset of `dataset1` containing only cells also found in `dataset2`.

Transfer the .obs attribute from one AnnData object to another, ensuring compatibility in .obs dimensionality and preserving the .var DataFrame. This function is designed to maintain the integrity of the target dataset’s gene expression information while enriching it with the metadata from the source dataset. It is a crucial step in the harmonization process, allowing for integrated analysis of datasets from different sources.

source

transfer_obs

 transfer_obs (dataset1:anndata._core.anndata.AnnData,
               dataset2:anndata._core.anndata.AnnData)

Transfer .obs metadata from dataset1 to dataset2 one by one, while preserving the .var DataFrame of dataset2.

	Type	Details
dataset1	AnnData	Source AnnData object with .obs metadata to transfer.
dataset2	AnnData	Target AnnData object to receive .obs metadata.
Returns	AnnData	The modified `dataset2` with .obs from `dataset1` transferred.