Download and install the package (containing all material) for use with R-3.1.0 / Bioconductor 2.14.
Install the course package with
source("http://bioconductor.org/biocLite.R")
dependencies <- c("Biostrings", "ShortRead", "ggplot2")
biocLite(dependencies)
install.packages("BiocIntro_0.0.3.tar.gz", repos=NULL)
Optionally, install suggested packages (used in exercises, etc) with
source("http://bioconductor.org/biocLite.R")
suggested <- c("BiocStyle", "knitr", "AnnotationHub",
"BSgenome.Hsapiens.UCSC.hg19", "BiocParallel", "Biostrings",
"GenomicAlignments", "GenomicFeatures", "GenomicRanges",
"Gviz", "IRanges", "PSICQUIC", "RNAseqData.HNRNPC.bam.chr14",
"TxDb.Hsapiens.UCSC.hg19.knownGene", "VariantAnnotation",
"biomaRt", "knitr", "org.Hs.eg.db", "parallel", "rtracklayer")
biocLite(suggested)
Explore the material through the following documents:
Introduction
Working with R
Sequencing work flows
Bioconductor for Sequence Analysis
- pdf, R, Rnw Bioconductor - Slides
- pdf, R, Rnw Genomic Ranges - Slides
- pdf, R, Rnw Working with DNA Sequences
- pdf, R, Rnw Working with FASTQ, BAM, and VCF files
- pdf, R, Rnw Working with Genomic Ranges
RNA-Seq
- pdf, R, Rnw RNASeq Analysis
- Exercises: see the RNA-seq Differential Expression Lab
Annotation and visualization