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A Statistical Web-Enabled Tool for the Identification of Significant Protein Coding Regions. Here, we present WISCOD, a web-enabled tool for the identification of significant protein coding regions, a novel software tool that tackles the exon prediction problem in eukaryotic genomes. WISCOD has the capacity to detect real exons from large lists of potential exons, and it provides an easy way to use global p-values called expected probability of being a false exon (EPFE) that is useful for ranking potential exons in a probabilistic framework, without additional computational costs. The advantage of our approach is that it significantly increases the specificity and sensitivity (both between 80% and 90%) in comparison to other ab initiomethods (where they are in the range of 70–75%). WISCOD is written in JAVA and R and is available to download and to run in a local mode on Linux and Windows platforms. (BioMed Research International Volume 2014, Article ID 282343, 10 pages).
CompARE is a free on-line platform developed to help investigators to choose the primary endpoint of a Randomized Clinical Trial. It analyzes whether you should use a Composite endpoint as Primary endpoint in time-to-event studies, comparing different scenarios depending on different candidate endpoints. It is of great help when planning a clinical trial since it quantifies how efficient is a relevant subset of outcomes respect to a larger subset of outcomes. CompARE is a friendly free tool, and, although is internally programmed in R, users do not need knowledge of R, neither to have R installed in their computer. CompARE is based on the free software Tightly Integrated Knowledge Infrastructure (Tiki Wiki CMS/Goupware). Tiki allows to execute R routines by means of the pluginR, software written under the GNU/LGPL license. By means of web-page forms, users can easily introduce the required information, step by step. This information is saved in trackers allowing the code to be executed by the system and returning ad-hoc results depending on each case. Results from CompARE are shown by means of summary tables and plots. A history table saves each result to compare previous analyses. Moreover, conclusions and recommendations are given in written form as an aid.
Statistics for Chromosome Interphase Positioning based on interchange data. The position of chromosomes in the interphase nucleus is believed to be associated with a number of biological processes. Here, we present a web-based application that helps analyze the relative position of chromosomes during interphase in human cells, based on observed radiogenic chromosome aberrations. The inputs of the program are a table of yields of pairwise chromosome interchanges and a proposed chromosome geometric cluster. Each can either be uploaded or selected from provided datasets. The main outputs are p-values for the proposed chromosome clusters. SCHIP is designed to be used by a number of scientific communities interested in nuclear architecture, including cancer and cell biologists, radiation biologists and mathematical/computational biologists. (Bioinformatics 21(14), 3181-3182).
Easy HeatMaps
A web tool to produce simple heatmaps for microarray data.