Bioconductor overview slides, HTML, PDF, Rmd

Bioconductor ExpressionSet exercise, PDF, Rmd, R

GEO exercise, PDF, Rmd

Annotation exercise, PDF, Rmd

Annotation exercise, PDF, Rmd

Filtering exercise, PDF, Rmd

• Data package, “SummarizedExperiment” single cell RNA-Seq data, human glioblastoma tissue. Paper: Patel et.al. http://science.sciencemag.org/content/344/6190/1396. Package: https://github.com/willtownes/patel2014gliohuman

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. doi:10.1186/gb-2004-5-10-r80. https://www.ncbi.nlm.nih.gov/pubmed/15461798 - The original Bioconductor publication

• 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 12, no. 2 (February 2015): 115–21. doi:10.1038/nmeth.3252. https://www.ncbi.nlm.nih.gov/pubmed/25633503 - Details of the latest Bioconductor development and functionality

• Bioconductor cheat sheet, covers basics of R/Bioconductor. Especially useful are sections about GenomicRanges and related commands. https://github.com/mikelove/bioc-refcard