City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. Please note: 1) The standalone version of COHCAP is no longer being updated. Please see the Bioconductor version: http://bioconductor.org/packages/release/bioc/html/COHCAP.html 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Bioconductor Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download
Bidirectional Functional Enrichment of Gene Expression Data
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
The purpose of eAudit is to provide a comprehensive reporting capability relating to Electronic Auditing for various industries.
An electronic application through which individuals can access, manage and share their health information, and that of others for whom they are authorized, in a private, secure, and confidential environment.
Tinymotion is an dedicated motion control hardware/software combo for cnc machine control applications. http://www.tinycontrols.com
This software is developed by Kalidas (http://openwetware.org/wiki/Kalidas_Y) as part of his Ph.D. thesis. The method enables alignment of ligand molecules considered molecular graphs. It is useful in the domain of drug discovery and bioinformatics.
GIS data for Greece has been scarce. This project aims to provide methods, instructions and data for the construction of environmental maps of Greece with the help of open source GIS tools.
PocketDepth helps determine binding grooves for protein molecules. Applicable in Bioinformatics and Drug discovery. Literature - http://www.ncbi.nlm.nih.gov/pubmed/17949996 Author's thesis - http://openwetware.org/wiki/Kalidas_Y
Association de l'asie pacifique et de l'asie mineur : Mention projet \apac (SF.NET) Chancellerie fédérale Palais fédéral ouest 3003 Berne
VEIN is a network analysis package written in Ruby. It is designed to be lightweight, scriptable and easy to use.
An encryption algorithm and UI frontend written in Java.
Mel McGee's Talkbots is a complete multi-browser, multi-platform talking head application in SVG suitable for web sites, or as an avatar for your programs. Text to speech (TTS) synthesis is sent using optional MP3 audio to lip synch ing characters.