{ "_id": "6ad85c314b18b9008999a5e2", "Package": "OncoSeq", "Type": "Package", "Title": "End-to-End Analysis of Cancer Transcriptomes and Genomes", "Version": "0.99.1", "Authors@R": "person(given = \"Umar\", family = \"Ahmad\",\nemail = \"babasaraki@yahoo.co.uk\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-3216-5171\"))", "Description": "OncoSeq provides a unified, end-to-end workflow for cancer\ntranscriptomic and genomic data analysis. A single container\nclass couples bulk RNA-sequencing counts with somatic mutation\ncalls, gene-level copy-number alterations and clinical\nfollow-up for the same set of tumour samples. The package\ncovers data import from the Genomic Data Commons, cBioPortal\nand local quantification files; quality control and filtering;\nnormalisation; differential expression through DESeq2, edgeR or\nlimma-voom behind one interface; gene-set enrichment and\nover-representation testing; Kaplan-Meier and Cox survival\nmodelling including genome-wide survival screens; mutation and\ncopy-number summarisation; integration of genomic alterations\nwith expression; and publication-ready visualisation. 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