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- Learning R / Bioconductor for Sequence Analysis
Learning R / Bioconductor for Sequence Analysis
Seattle, USA
2014-10-27 ~ 2014-10-29
Instructors
- Sonali Arora
- Nathaniel Hayden
- Martin Morgan
- Hervé Pagès
- Marc Carlson
- Valerie Obenchain
- Dan Tenenbaum
- Paul Shannon
Description
This course is directed at beginning and intermediate users who would like an introduction to the analysis and comprehension of high-throughput sequence data using R and Bioconductor. Day 1 focuses on learning essential background: an introduction to the R programming language; central concepts for effective use of Bioconductor software; and an overview of high-throughput sequence analysis work flows. Day 2 emphasizes use of Bioconductor for specific tasks: an RNA-seq differential expression work flow; exploratory, machine learning, and other statistical tasks; gene set enrichment; and annotation. Day 3 transitions to understanding effective approaches for managing larger challenges: strategies for working with large data, writing re-usable functions, developing reproducible reports and work flows, and visualizing results. The course combines lectures with extensive hands-on practicals; students are required to bring a laptop with wireless internet access and a modern version of the Chrome or Safari web browser.
Materials
Download the package (containing all material) for use with R-3.1.1 / Bioconductor 3.0.
Install the course package with
install.packages("LearnBioconductor_0.1.6.tar.gz", repos=NULL)
Optionally install suggested packages (used in exercises, etc.)
source("http://bioconductor.org/biocLite.R")
biocLite(c("knitr", "BiocStyle", "BiocInstaller", "ALL",
"BSgenome.Hsapiens.UCSC.hg19", "BiocParallel", "Biostrings",
"GenomicAlignments", "GenomicFeatures", "Gviz", "MLSeq",
"PoiClaClu", "RColorBrewer", "RNAseqData.HNRNPC.bam.chr14",
"Rsamtools", "ShortRead", "TxDb.Hsapiens.UCSC.hg19.knownGene",
"VariantAnnotation", "airway", "class", "cn.mops",
"dendextend", "fission", "genefilter", "ggplot2", "gplots",
"org.Hs.eg.db", "sva", "xtable", "PoiClaClu", "sva",
"fission", "kernlab", "e1071"))
Explore the material through the following documents:
- html, R, Rmd Introduction
- html, R, Rmd Introduction to R
- html, R, Rmd Introduction to Bioconductor
- html, R, Rmd Bioconductor for Sequence Analysis
- html, R, Rmd RNA-Seq Work Flows
- html RNA-Seq Lab
- html, R, Rmd Other Sequence Analysis Work Flows
- html, R, Rmd Machine Learning
- html, R, Rmd Annotating Genes, Genomes,and Variants
- html, R, Rmd Gene Set Enrichment
- html, R, Rmd Working With Large Data
- html, R, Rmd Organizing Code in Functions, Files ,and Packages
- html, R, Rmd Reproducible Research
- html, R, Rmd Visualization
- html, R, Rmd hg19_alias.tab Appendix: Install IGV