OncoSeq - End-to-End Analysis of Cancer Transcriptomes and Genomes

OncoSeq provides a unified, end-to-end workflow for cancer transcriptomic and genomic data analysis. A single container class couples bulk RNA-sequencing counts with somatic mutation calls, gene-level copy-number alterations and clinical follow-up for the same set of tumour samples. The package covers data import from the Genomic Data Commons, cBioPortal and local quantification files; quality control and filtering; normalisation; differential expression through DESeq2, edgeR or limma-voom behind one interface; gene-set enrichment and over-representation testing; Kaplan-Meier and Cox survival modelling including genome-wide survival screens; mutation and copy-number summarisation; integration of genomic alterations with expression; and publication-ready visualisation. Every analysis is recorded in the object so that a complete study can be reproduced from one object.