:: DESCRIPTION
LSGSP is the java codes which provided for use on this site are not part of the book Large-Scale Genome Sequence Processing published by Imperial College Press
::DEVELOPER
Masahiro Kasahara & Shinichi Morishita
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
WASP is a software covering the full range of analysis steps of a typical single-cell RNA sequencing workflow for Drop-Seq-based scRNA-Seq data.
::DEVELOPER
Bioinformatics and Systems Biology, Justus-Liebig-University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hoek A, Maibach K, Özmen E, Vazquez-Armendariz AI, Mengel JP, Hain T, Herold S, Goesmann A.
WASP: a versatile, web-accessible single cell RNA-Seq processing platform.
BMC Genomics. 2021 Mar 18;22(1):195. doi: 10.1186/s12864-021-07469-6. PMID: 33736596; PMCID: PMC7977290.
:: DESCRIPTION
SeqTrace is an application for viewing and processing DNA sequencing chromatograms (trace files). SeqTrace makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA.
::DEVELOPER
Brian J. Stucky stuckyb@colorado.edu , Guralnick Lab
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Biomol Tech. 2012 Sep;23(3):90-3. doi: 10.7171/jbt.12-2303-004.
SeqTrace: a graphical tool for rapidly processing DNA sequencing chromatograms.
Stucky BJ.
:: DESCRIPTION
MorphoGraphX is a cross-platform, open-source application for the visualization and processing of 3D biological datasets.
::DEVELOPER
Richard S. Smith ,Systems Biology/Developmental Modeling
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Methods Mol Biol. 2014;1080:121-34. doi: 10.1007/978-1-62703-643-6_10.
Quantifying cell shape and gene expression in the shoot apical meristem using MorphoGraphX.
de Reuille PB1, Robinson S, Smith RS.
Daniel Kierzkowski et al.
Elastic Domains Regulate Growth and Organogenesis in the Plant Shoot Apical Meristem
Science 2 March 2012: Vol. 335 no. 6072 pp. 1096-1099
:: DESCRIPTION
The MIPAV application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. Using MIPAV’s standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Neurosci Methods. 2007 Sep 15;165(1):111-21. Epub 2007 May 29.
Volumetric neuroimage analysis extensions for the MIPAV software package.
Bazin PL, Cuzzocreo JL, Yassa MA, Gandler W, McAuliffe MJ, Bassett SS, Pham DL.
:: DESCRIPTION
snapCGH is a softwaer for the analysis of array CGH data. It has been written to be compatible with limma so that the user can apply all of the preprocessing functions available within limma to array CGH data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
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
::DEVELOPER
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Res Notes. 2013 Jan 4;6:5. doi: 10.1186/1756-0500-6-5.
ASAP: an environment for automated preprocessing of sequencing data.
Torstenson ES1, Li B, Li C.
:: DESCRIPTION
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
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2011 Mar 15;27(6):867-9. doi: 10.1093/bioinformatics/btr012. Epub 2011 Jan 13.
A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.
:: DESCRIPTION
RPASuite is a computational pipeline to identify differentially and coherently processed transcripts using RNA-seq data obtained from multiple tissue or cell lines.
::DEVELOPER
Center for non-coding RNA in Technology and Health (RTH)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pundhir S and Gorodkin J. (2015)
Differential and coherent processing patterns from small RNAs.
Sci Rep. 5:12062
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Olivier Filangi at el. 2008
BioMAJ: A flexible framework for databanks synchronization and processing
Bioinformatics 2008 24(16):1823-1825;
