FGDP: functional genomics data pipeline for automated, multiple microarray data analyses

Hal: an Automated Pipeline for Phylogenetic Analyses of Genomic Data

The rapid increase in genomic and genome-scale data is resulting in unprecedented levels of discrete sequence data available for phylogenetic analyses. Major analytical impasses exist, however, prior to analyzing these data with existing phylogenetic software. Obstacles include the management of large data sets without standardized naming conventions, identification and filtering of orthologous...

Functional genomics by data mining in DNA microarray data

The DNA microarray is a new tool for rapid and efficient collection of gene expression data. Several thousand genes can be tested simultaneously, and up or down regulation of genes as a function of time and changes in experimental conditions can easily be identified. Such changes may be external stress, disease (e.g. cancer), drugs or simply natural development. From this information networks o...

cDNA Microarray Data Normalization

Linear Models for Functional Data

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Pipeline for macro- and microarray analyses.

The pipeline for macro- and microarray analyses (PMmA) is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). It can also be used as a plugin in ...