ASAP (Advanced Sequence Automated Pipeline)is an open source pipeline designed to assist users in managing various jobs associated with processing HiSeq data on a cluster or in serial. . The software was designed to alleviate these issues by providing a modular system to allow users with different needs to process their data with a minimal amount of effort. In addition to minimizing human involvement, ASAP is designed to work on the researcher’s local computer cluster, if one is available
ArrayExpressHTS is an R and Bioconductor RNA-seq processing pipeline that highly utilizes distributed computing for data processing and quality assessment of High-Throughput Sequencing experiments and datasets
BioMAJ (BIOlogie Mise A Jour) is a workflow engine dedicated to data synchronization and processing. The Software automates the update cycle and the supervision of the locally mirrored databank repository.
SePIA is a comprehensive RNA Sequencing workflow standardizing Processing, Integration, and Analysis of large-scale sequencing data. It provides a systematic, pipeline architecture to manage, individually analyze, and integrate both small-RNA and RNA data.
BioC is a simple XML format to share text documents and annotations. It allows a large number of different annotations to be represented. We provide simple code to hold this data, read it and write it back to XML files, and perform some sample processing.
Youngsong Cho, Jae-Kwan Kim, Joonghyun Ryu, Chung-In Won, Chong-Min Kim, Donguk Kim, and Deok-Soo Kim,
BetaMol: a molecular modeling, analysis and visualization software based on the beta-complex and the quasi-triangulation,
Journal of Advanced Mechanical Design, Systems, and Manufacturing, Vol.6, Issue 3, pp. 389-403, 2012
RobiNA is an integrated solution that consolidates all steps of RNA-Seq-based differential gene-expression analysis in one user-friendly cross-platform application featuring a rich graphical user interface. RobiNA accepts raw FastQ files, SAM/BAM alignment files and counts tables as input. It supports quality checking, flexible filtering and statistical analysis of differential gene expression based on state-of-the art biostatistical methods developed in the R/Bioconductor projects. In-line help and a step-by-step manual guide users through the analysis.