Bioconductor
References
Gentleman, Robert C., Vincent J. Carey, Douglas M. Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, et al. “Bioconductor: Open Software Development for Computational Biology and Bioinformatics.” Genome Biology 5, no. 10 (2004): R80.
Huber, Wolfgang, Vincent J. Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S. Carvalho, Hector Corrada Bravo, et al. “Orchestrating High-Throughput Genomic Analysis with Bioconductor.” Nature Methods, (February 2015) - Bioconductor overview
Ramos, Marcel, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez Cabrera, Tiffany Chan, et al. “Software For The Integration Of Multi-Omics Experiments In Bioconductor,” June 1, 2017. - MultiAssayExperiment, Bioconductor package for management of multi-assay data
Lawrence, Michael, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T. Morgan, and Vincent J. Carey. “Software for Computing and Annotating Genomic Ranges.” PLoS Computational Biology, (2013) - IRanges, GenomicRanges, GenomicFeatures packages.
Bioconductor resources
“Bioconductor for Genomics Data Science” course by Kasper Hansen. IRanges, GRanges, seqinfo, AnnotationHub, Biostrings, BSgenome, rtracklayer, and more. Includes videos, code examples and lecture material. GitHub
Introduction to Computational Biology course by Mike Love. GitHub
Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment - workshop by Levi Waldron’s group