Pretraining Improves Prediction of Genomic Datasets Across Species.

Official website: http://bio-bwa.sourceforge.net/

TopHat 2.0.14 using Bowtie 2.2.3

Differential gene expression analysis based on the negative binomial distribution.

docker image of PredictionIO-0.10.0, and PredictionIO-0.12.0(latest stable version of PreditionIO)

RiboPicker allows to identify and remove rRNA from metagenomic datasets (ribopicker.sourceforge.net)

A lims system to automate and expedite proteomics data management, processing and analysis. The CompOmics LIMS system, designed as the next-generation version of the ms_lims system, including much more powerful processing and analysis tools, and sporting a fully self-contained, freely available system for end-to-end mass spectrometry based proteomics identification pipelines.