This directory contains the R files used for the course of Statistics Applied to Bioinformatics.
source('http://www.bigre.ulb.ac.be/courses/statistics_bioinformatics/Rfiles/config.R')
Installation and configuration  

install_packages.R  Installation of some R packages used for the course 
config.R  Defines the configuration (directories, web site, ...), creates the directory to store the results of the practicals, and load the general utilities. This script should be sourced before other scripts. 
Descriptive statistics  
central_tendency_dna_chip.R  Plot distribution of a DNA chip experiment 
central_tendency_yeast_orf_lengths.R  Plot distribution of yeast ORF lengths 
Theoretical distributions  
geometric.R  Geometric distribution (figures) 
hypergeometric_series.R  Hypergeometric distribution (figures) 
hypergeometric_recursion.R  Recursive computation of the hypergeometric 
hypergeometric_versus_binomial.R  Comparison between hypergeometric and binomial (table + figure) 
binomial.R  Figure with the binomial density and distribution function 
binomial_series.R  Series of binomial distributions: effect of the probability of succcess at each trial (p) 
poisson_series.R  Series of Poisson distributions: effect of the mean 
binomial_to_normal.R  Series of binomial distributions with an increasing number of trials, to illustrate convergence towards the normal distribution 
student.R  Series of Student distributions with increasing degrees of freedom, to illustrate the convergence towards the normal distribution. 
Sampling and estimation  
sampling_mean_distribution.R  Illustration of the effect of sample size on the variance of the mean estimate. 
Fitting  
fitting_normal_examples.R  Histograms with the fitting of a normal curve on different data sets 
Hypothesis testing  
conformity_tests.R  Illustrations of the conformity tests.

student_test.R  Student test, multiple testing  select differentially expressed genes in a microarray data experiment (Golub 1999). 
Utilities  
util/util.R  General utilities (export scripts) 
util/util_descr_stats.R  Descriptive statistics 
util/util_central_tendency.R  Plot a histogram with the indication of central tendency and dispersion parameters 
util/util_student_test_multi.R  Efficient implementation to apply the Student test (Welch version) to each row of an array. 
util/util_test_fitting_binomial.R  Test the fitting of a binomial distribution on a sample distribution. 
util/util_test_fitting_poisson.R  Test the fitting of a Poisson distribution on a sample distribution. 
util/util_test_fitting_normal.R  Test the fitting of a normal distribution on a sample distribution. 
util/util_chip_analysis.R  Plot gene expression profiles, Kmean clustering with profiles, SVD plot. 
Clustering  
clustering_kmeans.R  Illustrations of mobile canters and Kmeans clustering 
clustering_carbon_sources.R  Illustration of clustering (hierarchiacl and Kmeans) with Gasch data (yeast growth with different carbon sources) 
Examples of microarray data analysis  
spellman98/  Directory with the R scripts fir the analysis of cell cycle data from Spellman 1998 
load_spellman.R  load cell cycle data from Spellman 1998 
spellman_analysis.R  Kmeans profiles and SVD with cell cycle data from Spellman 1998 
Solutions to the exercises of the practicals  
exercises/word_count_distrib.R  Fitting 
Solutions to the exercises from the book  
exercises_probabilities.R  Probabilities 
Theoretical distributions  
Hypothesis testing  
Significance tests  
Discriminant analysis 