.. modality documentation master file, created by sphinx-quickstart on Wed Jan 17 11:44:25 2024. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. modality documentation **modality** is a powerful and versatile Python tool designed for the analysis of methylation data. Leveraging the capabilities of `dask `_ for chunked computation and `xarray `_ for multi-dimensional data interaction, modality offers a fast, memory-efficient, and parallelizable solution for a range of methylation data analyses. Key Features ------------ - **Summarize Methylation Information:** modality facilitates the extraction of methylation information (such as fractions, means, etc...) across genomic regions (such as exons, genes, TSS, and more). Users can easily aggregate methylation data across various dimensions, providing a comprehensive overview of methylation patterns. - **Efficient Subset and Plotting:** With modality, users can efficiently subset methylation data and generate plots, traces, and histograms. This functionality enables users to visualize and explore methylation patterns, and perform basic QC of their data (e.g. CpG coverage). - **Genomewide Correlation analysis:** modality facilitates the analysis of genomewide correlation (such as the computation of Pearson correlation between samples either genomewide or over specific regions of interest), allowing the user to assess methylation correlations across samples. - **Differential Methylation Analysis (DMRs):** modality is equipped to identify differentially methylated regions (DMRs) across a cohort, aiding researchers in pinpointing genomic regions with significant methylation variations. Users can utilise modality's DMR toolkit to quickly call and visualize epigenetic changes associated with various biological conditions or experimental treatments. Performance Highlights ---------------------- - **Parallel Processing and memory efficiency:** modality leverages the parallel processing capabilities of `dask `_ to handle large methylation datasets efficiently. This ensures that analyses are not only fast but also scalable to accommodate diverse experimental designs. - **Multi-dimensional Data Interaction:** Using `xarray `_, modality enables users to interact with methylation data seamlessly across multiple dimensions (e.g., reference position of CpG, sample ID, and more). This flexibility enhances the versatility of analyses and allows for in-depth exploration of complex datasets. - **Easy Integration with zarr:** modality is designed to be easily integrated with `zarr `_, a Python package for chunked, compressed, N-dimensional arrays. This feature enables users to store and access methylation data efficiently, even when working with large datasets. .. raw:: html **modality** is a powerful and versatile Python tool designed for the analysis of methylation data. .. toctree:: :maxdepth: 1 :caption: Contents Contents -------- .. toctree:: :maxdepth: 1 installation getting_started examples modality modality_cli Indices and tables ------------------ * :ref:`genindex` * :ref:`modindex` * :ref:`search` .. raw:: html