Search Results for "algorithm"

BD-Func is an algorithm to predict activation or inhibition of pathways based upon gene expression patterns. If you use BD-Func, please cite: Warden C, Kanaya N, Chen S, and Yuan Y-C. (2013) BD-Func: A Streamlined Algorithm for Predicting Activation and Inhibition of Pathways. peerJ, 1:e159

COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub...

Flip card learning program for iPhone with a spaced learning algorithm. Create your own databases and edit the cards directly on the iPhone. Import Palm databases or csv-formatted files and backup your data with our Java application.

FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.

HIVCD is an informatics tool developed to identify patient sequences that are too similar to happen by chance alone. Highly similar sequences are likely to occur from contamination or other situations like geographic linkage. Full details can be found in our paper titled "Application of a new informatics tool for contamination screening in the HIV sequencing laboratory" The code provided is a simple user interface to the underlying algorithm. We provide it as a convenience but it comes...

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74

A collection of implementations of the Lovins stemmer as described in "Development of a Stemming Algorithm" by Julie Beth Lovins (published in "Mechanical translation and computational linguistics", 11:22-31, 1968).

The goal of the Rats and Mazes project is to build a simple genetic algorithm to find general solutions to random non-cyclic single path mazes. I believe that the solutions will tend towards either the right/left-hand rule.

A repository of grid computing student exercises. The repository currently contains a grid-enabled mergesort using Condor. Exercises to be developed include genome analysis, genetic algorithm, integration, matrix multiply, ray tracing, etc.