Added GEO Matrix file support for downloading and parsing expression data #232
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- Added GEOMatrix class for handling GEO Matrix files, including methods for downloading, parsing, and converting to DataFrame and TSV. - Extended GEOweb class to identify and download matrix files from GEO FTP. - Introduced new CLI command `geo-matrix` for downloading and processing GEO Matrix files. - Updated existing `download` command to support downloading only matrix files with `--matrix-only` flag. - Enhanced README and documentation to include GEO Matrix file support and usage examples. - Created tests for GEOMatrix functionality, including link retrieval, file downloading, parsing, DataFrame conversion, and TSV export.
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Closes #229
This PR adds support for GEO Matrix files, which contain processed expression data from NCBI's Gene Expression Omnibus.
Features Added
GEOMatrixclass for downloading and parsing matrix files.GEOwebclass with matrix-specific methods.geo-matrixfor matrix operations.--matrix-onlyoption to the existingdownloadcommand.Example Usage
CLI
Python API