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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Software-as-a-service for big data management offering fast, reliable, secure file transfer and sharing services to non-profit researchers. It combines state-of-the-art algorithms, data management tools, a graphical workflow environment, and an elastic computing infrastructure making it easy to manipulate, store, and share your data, no matter how big it gets.
Proper citation: Globus Genomics (RRID:SCR_011887) Copy
Public research university in Richmond, Virginia. MCV was founded in 1838 as the medical department of Hampden–Sydney College, becoming the Medical College of Virginia in 1854.
Proper citation: Virginia Commonwealth University; Virginia; USA (RRID:SCR_011767) Copy
http://ebardenovo.sourceforge.net/
Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.
Proper citation: EBARDenovo (RRID:SCR_011890) Copy
http://i.cs.hku.hk/~alse/hkubrg/projects/idba_tran/
An iterative De Bruijn Graph De Novo short read assembler for transcriptome.
Proper citation: IDBA-Tran (RRID:SCR_011891) Copy
Private research university in Winston-Salem, North Carolina.
Proper citation: Wake Forest University; North Carolina; USA (RRID:SCR_011772) Copy
It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis.
Proper citation: Oqtans (RRID:SCR_011905) Copy
http://bioinfo.au.tsinghua.edu.cn/software/RNAseqViewer/
Software to visualize the various data from the RNA-Seq analyzing process, for single or multiple samples.
Proper citation: RNAseqViewer (RRID:SCR_011900) Copy
http://transcriptome.ens.fr/eoulsan/
A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.
Proper citation: Eoulsan (RRID:SCR_011901) Copy
A user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing.
Proper citation: FX (RRID:SCR_011902) Copy
http://utgenome.org/index.html
An open-source software for developing personalized genome browsers that work in web browsers.
Proper citation: UTGB Toolkit (RRID:SCR_011797) Copy
http://www.cisd.ethz.ch/software/openBIS
Software for an open, distributed system for managing biological information that supports biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: * High Content Screening * Proteomics * Deep Sequencing * Metabolomics
Proper citation: openBIS (RRID:SCR_011815) Copy
Graphical user interface software for metadata-driven management, analysis, and visualization of microbiome data.
Proper citation: Explicet (RRID:SCR_011937) Copy
An online toolbox for metagenomic data visualization.
Proper citation: MetaSee (RRID:SCR_011938) Copy
http://genopole.pasteur.fr/SynTView/
An interactive multi-view genome browser for next-generation comparative microorganism genomics.
Proper citation: SynTView (RRID:SCR_011939) Copy
http://www.ebi.ac.uk/Tools/msa/kalign/
A fast and accurate multiple sequence alignment algorithm.
Proper citation: Kalign (RRID:SCR_011810) Copy
http://ccb.jhu.edu/software/glimmer/index.shtml
A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
Proper citation: Glimmer (RRID:SCR_011931) Copy
http://mafft.cbrc.jp/alignment/server/
Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
Proper citation: MAFFT (RRID:SCR_011811) Copy
http://bioen-compbio.bioen.illinois.edu/PSAR-Align/
Software for improving multiple sequence alignment using probabilistic sampling.
Proper citation: PSAR-Align (RRID:SCR_011814) Copy
http://www.csd.uwo.ca/~ilie/HiTEC/
Accurate error correction in high-throughput sequencing data.
Proper citation: HiTEC (RRID:SCR_011826) Copy
http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php
A Next-Generation Sequencing Simulator for Metagenomics.
Proper citation: NeSSM (RRID:SCR_011941) Copy
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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