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As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/

Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project. MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data....

The goal of the Perl OBD-II Logger project is to create a flexible and efficient application that can capture and log OBD-II Mode 0x01 PID data from an automotive scantool. It is designed with accurate and efficient PID data logging in mind, and provides NO support for reading or resetting diagnostic trouble codes. By default, the output log file contains time-stamped PID values in a simple Comma Separated Values (CSV) format that can be readily imported into popular data analysis or spreadsheet applications. ...

Project moved to https://github.com/ivandeex/optikus

The Canopy project is an initiative to merge and expand the functionality of Perl-speaks-NONMEM (PsN), Census, Xpose and PopED. The goal is to produce a coherent, inclusive and convenient platform for pharmacometric data analysis.

graphite: a portable graphics library, written in Java, JOGL and Postscript that allows rapid generation of high-quality graphs using an efficient, compact Java engine.