Instructor: Kasper Daniel Hansen
Email: khansen@jhsph.edu
Office: SPH E3648
Office: MRB 453
Course webpage: http://www.biostat.jhsph.edu/~khansen/teaching/2014/140.668
Course email list (also a google group):
TA: Jean-Philippe Fortin
Email: jfortin@jhsph.edu
SPH 4007
Tu 1.30-2.50
Th 1.30-2.50
Th 3-4, SPH E3648
Fr 10-12, SPH E3607, The Genome Cafe
Due Monday 5/26. Length: 4 pages + 5 display items + references, in PDF format.
The books below are all freely available as PDFs when accessed through "SpringerLink" inside the campus network. This makes them extremely good value for money.
WN Venables, DM Smith and the R Core Team (2014) An Introduction to R.
PDF
A Short and concise introduction to R. At times it is too brief; it is worthwhile to fully understand everything in the text. Ships with R.
F. Hahne, W Huber, R Gentleman and S Falcon (2008) Bioconductor Case Studies.
SpringerLink
The latest Bioconductor monography. Each chapter is an analysis task. Some things are surely dated by now, but it should still be studied.
Peter Dalgaard (2008) Introductory Statistics with R.
SpringerLink
This is a classic (easy) book on Biostatistics and R.
M Allerhand (2011) A Tiny Handbook of R.
SpringerLink
I have not read this book, but it is short, which is always good.
There are a number of additional books on R in the useR Springer Series. Several seems introductory of nature.
Why
Biology
Statistics
Collection Data, a Story
Microarray Technology
Microarray Preprocessing
Design of Experiments
Differential expression
Multiple testing
Clustering
Batch effects
Sequencing and alignment
Gene Regulation (ChIP-seq)
ChIP-PED (ChIP-seq)
dPCA (ChIP-seq)
DNA methylation and the CHARM assay
Analysis of Bisulfite converted data
GenomeArithmetic
IRanges
Genomic correlation