https://babasaraki.r-universe.devRecent package updates in babasarakiR-universehttps://github.com/babasaraki.pnghttps://babasaraki.r-universe.devWed, 21 Oct 2026 04:29:39 GMTbabasaraki@yahoo.co.uk (Umar Ahmad)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.https://github.com/r-universe/biocstaging/actions/runs/39553898539Wed, 21 Oct 2026 04:29:39 GMTOncoSeq0.99.1successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/OncoSeqOncoSeq.RmdOncoSeq.htmlAnalysing cancer transcriptomes and genomes with OncoSeq2026-10-20 09:40:522026-10-20 09:40:52