Statistics for Bioinformatics - links

Program URL Platforms Distribution Category Description
R http://www.r-project.org/ Unix, Macintosh, Windows Open source Statistics One of the most famous statistical packages. Many librairies, including specific ones for the analysis of microarray data.
R Unix, Macintosh, Windows Web site DAVID The Database for Annotation, Visualization and Integrated Discovery (DAVID ). DAVID can be used to perform functional annotation of gene lists.
Bedtools Unix, Macintosh Open source Genomics The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together.
YASMA http://people.cryst.bbk.ac.uk/wernisch/yasma.html
Bioconductor http://www.bioconductor.org/ R package Open source Biostatistics An open source and open development software project for the analysis and comprehension of genomic data.
TIGR Microarray suite TM4 http://www.tigr.org/software/tm4/ Java or C++ for Windows Open source Microarrays The TM4 suite of tools consist of four major applications, Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System(MIDAS), and Multiexperiment Viewer(MeV)
TIGR MIDAS http://www.tigr.org/software/tm4/midas.html Java Open source Normalization TIGR Microarray Data Analysis System (MIDAS) is a microarray data quality filtering and normalization tool that allows raw experimental data to be processed through various data normalizations, filters, and transformations via a user-designed analysis pipeline. Currently implemented normalization and data analysis algorithms include total-intensity normalization, Lowess (Locfit) normalization, flip-dye consistency checking, replicates analysis, intensity-dependent z-score filtering (slice analysis), etc.
TIGR MeV http://www.tigr.org/software/tm4/mev.html Java Open source Clustering
Visualization
TIGR MultiExperiment Viewer (MEV) is a Java application designed to allow the analysis of microarray data to identify patterns of gene expression and differentially expressed genes. Numerous normalization, clustering and distance algorithms have been implemented, along with a variety of graphical displays to best present the results.
http://www.tigr.org/software/tm4/utilities.html Windows Freeware Converter utility ExpressConverter is a file format transformation tool that reads GenePix file as input and generates output as TIGR ArrayView file (.tav) or TIGR MultiExperiment Viewer file (.mev) so that the microarray data can be uploaded to databases with MADAM and analyzed with MIDAS and MEV.
BASE http://base.thep.lu.se/ Freeware BASE is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. It is released under the GNU General Public License. Further details about BASE can be found by following the links to the left or by reading the BASE manuscript (see below).
BRB ArrayTools http://linus.nci.nih.gov/BRB-ArrayTools.html Windows + Excel Freeware BRB ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. It was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments. The array tools package utilizes an Excel front end. Scientists are familiar with Excel and utilizing Excel as the front end makes the system portable and not tied to any database. The input data is assumed to be in the form of Excel spreadsheets describing the expression values and a spreadsheet providing user-specified phenotypes for the samples arrayed. The analytic and visualization tools are integrated into Excel as an add-in. The analytic and visualization tools themselves are developed in the powerful R statistical system, in C and Fortran programs and in Java applications. Visual Basic for Applications is the glue that integrates the components and hides the complexity of the analytic methods from the user. The system incorporates a variety of powerful analytic and visualization tools developed specifically for microarray data analysis.
ViDaExpert http://www.ihes.fr/~zinovyev/vida/vidaexpert.htm Windows Freeware Vizualisation Software tool for visualization of multidimensional datasets. It allows to make understandable color illustrations of a dataset to explore its intrinsic patterns and regularities. The main technique implemented in ViDaExpert is the Method of Elastic Maps advanced analogue of the Method of Self-Organizing Maps. Besides, there are many other methods of data analysis, including Principal Components Analysis, different clustering methods, Linear Discriminate Analysis, Linear Regression Method.