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xOmics (eXplainable Omics) is a Python framework developed for interpretable omics analysis, focusing on differential proteomics expression data. It introduces the following key algorithms:

• cImpute: Conditional Imputation - A transparent method for hybrid missing value imputation.
• pRank: Protein-centric ranking of (prote)omic data, including integration with functional enrichment results.
• pIntegrate: Protein-centric integration of multiple (prote)omic datasets for differential analysis.
• QARIP: Quantitative proteomic analysis of regulated intramembrane proteolysis.

In addition, xOmics provides functional capabilities for efficiently loading benchmark proteomics datasets via load_datasets, accompanied by corresponding enrichment data.A suite of supportive functions is also available to facilitate a smooth and efficient (prote)omic analysis pipeline.

xOmics can be installed either from PyPi or conda-forge:

pip install -u xomics
or
conda install -c conda-forge xomics

We appreciate bug reports, feature requests, or updates on documentation and code. For details, please refer to Contributing Guidelines. For further questions or suggestions, please email [email protected].

If you use xOmics in your work, please cite the respective publication as follows:

xOmics:

[Citation details and link if available]

cImpute:

[Citation details and link if available]

pRank:

[Citation details and link if available]

pIntegrate:

[Citation details and link if available]

QARIP:

QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis Nucleic Acids Research.