Bioconductor - Learning R / Bioconductor for Sequence Analysis

Download the package (containing all material) for use with R-3.1.1 / Bioconductor 3.0.

LearnBioconductor_0.1.6.tar.gz

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