London BioGeeks | Bioinformatics in London | Page 2

London BioGeeks Bioinformatics in London Page 2: "London BioGeeks
Bioinformatics in London"

DNA sequencing technologies

DNA sequencing technologies - tutorial on traditional and next-generation sequencing technologies

useful databases, genetic research, LD analysis

useful databases for genetic research ,

These sites are of potential interests for people carrying out LD analysis:

Nomenclature for the description of sequence variants

human genetic variation
nomenclature of genetic sequence changes, variants etc

intro R statistical package

intro courses in R

quick-R - a "must see" by dr Kabacoff,
also preparing book "R in action"

nice tutorial on R- pdf. 104pp by Matloff - Uni Davis

Oxford course by Ruth Ripley incl. slides, r files ....

Aarhus introduction course XXX- recommended books, course materials,
by Ulrich Halekoh, Søren Højsgaard, Asger R. Pedersen incl. R in Few Hours tutorial :)

Intro to R XXX - quite extensive pdf, datamanipulations, graphics, statistics, up to datamining.
by Statgenetics ... UAB ...UofAlabamaATbirmingham by Lumley T /member of R core develepment team
site includes some other pdf of exercise etc, and even video /videos only for Uni-members

Using R for statistical analyses - Introduction by dr Gardener - nice layout

MAT 356 R Tutorial, Spring 2004 - concise, many examples, inclusive plotting options, very instructive


advanced statistics - Exploratory Data Analysis (EDA) and Regression from astrophysicist
- includes a lot of code for different types of regression (linear, polynomial, ridge, spline .....), but no plot, or other output

genetic statistics SOFTWARE

LINKAGE AND LINKAGE DISEQUILIBRIUM

GENETIC STATISTICS, STATISTICAL GENETICS SOFTWARE
Following are the category of programs we have available for the analysis:
Association and TDT Programs
Error Checking Programs
Genome Wide Association Programs
Haplotyping Programs
Linkage Analysis Programs
Pedigree Drawing Programs
Population Genetics Programs
Segregation Programs
Simulation Programs
Stratification Programs
Utility Programs

linkage disequilibrium

linkage disequilibrium (LD)- basics, measures /D, Dprime, r_squared/, causes, of LD by Abecasis from U Michigan
- includes pros and cons and limitations of individual measures of LD !!!!

linkage disequilibrium - worked example of how to compute different measures, on causes etc.

"classical" brief note on LD - linkage vs linkage disequilibrium

paper on volume measures of LD - as part of intro describes calculation of D´and r2.