Course package (Morgan) EMBOBGI_0.0.2.tar.gz Download and install as follows in R-3.0, starting R in the directory where you downloaded the file:
biocLite(c("ggplot2", "Biostrings", "ShortRead"))
install.packages("EMBOBGI_0.0.2.tar.gz", repos=NULL, type="source")
Day 2
- NGS Challenges (Rustici) pdf
- R Basics (Huber) pdf R script
- R / Bioconductor Introduction (Morgan) pdf
- Working with Sequence Data in R / Bioconductor -- Exercises (Morgan) pdf, R script
Day 3
- Annotation (Morgan) pdf, R script
- RNA-seq Differential Expression Lab (Huber / Anders) pdf, R script, localUcscTable.csv
Day 4
- RNA-seq Differential Expression (Huber) pdf
- Multiple testing (Huber) pdf
- RNA-seq Differential Expression / Exon Use (Anders) pdf
- Ranges (Morgan) pdf, R-script
- Annotation and Ranges -- Exercises (Morgan) pdf, R-script
Day 5
- Gene Set Enrichment (Morgan) pdf
- Archiving NGS data (Rustici) pdf
- Ensembl Coursebook (Rustici) pdf
- Pathway Analysis (Rustici) pdf
- Reactome (Rustici) pdf
- Mapping (Liu) pdf
- Variation Detection (Liu) [pdf](VariationDetection-Xin Liu.pdf); drill [pdf](Drill-Xin Liu.pdf)
Day 6