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http://snver.sourceforge.net/

Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.

Proper citation: SNVer (RRID:SCR_002061) Copy   

•   Source: SciCrunch Registry

http://www.yandell-lab.org/software/vaast.html

A probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of phylogenetic conservation, amino acid substitution, and aggregative approaches to variant prioritization into a single unified likelihood-framework that allows users to accurately identify damaged genes and deleterious variants. The software can score both coding (SNV, indel and splice site) and non-coding variants (SNV), evaluating the cumulative impact of both types of variants simultaneously. It can identify rare variants causing rare genetic diseases and can also use both rare and common variants to identify genes responsible for common diseases.

Proper citation: VAAST (RRID:SCR_002179) Copy   

•   Source: SciCrunch Registry

http://cmb.gis.a-star.edu.sg/ChIPSeq/paperChIPSeq.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ChIPSeq Peak Finder (RRID:SCR_002081) Copy   

•   Source: SciCrunch Registry

http://genome.jgi.doe.gov/

Portal providing access to all JGI genomic databases and analytical tools, sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web.

Proper citation: JGI Genome Portal (RRID:SCR_002383) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/SNP/

Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.

Proper citation: dbSNP (RRID:SCR_002338) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/pyxnat/

Software Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data.

Proper citation: pyxnat (RRID:SCR_002574) Copy   

•   Source: SciCrunch Registry

http://www.paraview.org/

Open source, multi platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.

Proper citation: ParaView (RRID:SCR_002516) Copy   

•   Source: SciCrunch Registry

http://rubioseq.sourceforge.net/

Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments.

Proper citation: RUbioSeq (RRID:SCR_002508) Copy   

•   Source: SciCrunch Registry

http://genetics.bwh.harvard.edu/pph2/

Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.

Proper citation: PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ai.sri.com/ptools/

A software application which supplies software tools to develop and maintain pathway/genome databases (PGDBs). These include the development of organism-specific databases, metabolic reconstruction and metabolic-flux modeling, scientific visualization and web publishing of organism-specific databases, analysis of gene-expression and metabolomics datasets, comparative genome and pathway analyses, and analysis of biological networks.

Proper citation: Pathway Tools (RRID:SCR_013786) Copy   

•   Source: SciCrunch Registry

http://www.metabolomicsworkbench.org

Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops.

Proper citation: Metabolomics Workbench (RRID:SCR_013794) Copy   

•   Source: SciCrunch Registry

http://www.osirix-viewer.com/

:OsiriX is an image processing software dedicated to DICOM images (.dcm / .DCM extension) produced by medical equipment (MRI, CT, PET, PET-CT, ...) and confocal microscopy (LSM and BioRAD-PIC format). It can also read many other file formats: TIFF (8,16, 32 bits), JPEG, PDF, AVI, MPEG and Quicktime. It is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or medical imaging modality (STORE SCP - Service Class Provider, STORE SCU - Service Class User, and Query/Retrieve) . OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D Viewer, 3D Viewer, 4D Viewer (3D series with temporal dimension, for example: Cardiac-CT) and 5D Viewer (3D series with temporal and functional dimensions, for example: Cardiac-PET-CT). The 3D Viewer offers all modern rendering modes: Multiplanar reconstruction (MPR), Surface Rendering, Volume Rendering and Maximum Intensity Projection (MIP). All these modes support 4D data and are able to produce image fusion between two different series (for example: PET-CT). Osirix is at the same time a DICOM PACS workstation for medical imaging and an image processing software for medical research (radiology and nuclear imaging), functional imaging, 3D imaging, confocal microscopy and molecular imaging. :

Proper citation: OsiriX Medical Imaging Software (RRID:SCR_013618) Copy   

•   Source: SciCrunch Registry

http://blanco.biomol.uci.edu/mpex/

Software which predicts topology and other features of membrane proteins through hydropathy plots based on thermodynamic and biological principles. This version of MPEx uses two types of hydropathy scales: Experiment-based whole-residue partitioning scales and experiment-based biological partitioning scales. The whole-residue partitioning scales predict the transmembrane (TM) segments of membrane proteins of known structure. The biological scale utilizes current knowledge of the code the Sec61 translocon to identify TM segments. MPEx is a Java program (not a Java applet) deployed using Java Web Start, which is part of the Java Runtime Environment.

Proper citation: Membrane Protein Explorer (RRID:SCR_014077) Copy   

•   Source: SciCrunch Registry

http://www.ccp4.ac.uk/html/cbuccaneer.html

Software which performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target. The target distributions are generated by a simulation calculation using a known reference structure for which calculated phases are available. The success of the method is dependent on the features of the reference structure matching those of the unsolved work structure. For almost all cases, a single reference structure can be used, with modifications automatically applied to the reference structure to match its features to the work structure.

Proper citation: Buccaneer (RRID:SCR_014221) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/software/fluorender.html

Interactive rendering tool for confocal microscopy data visualization. Combines rendering of multi-channel volume data and polygon mesh data, where properties of each dataset can be adjusted independently and quickly. Designed for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples. Features include feature tracking, 3D measurement tools, multiple render modes for multi-channel confocal data, and volume paint selection and segmentation.

Proper citation: FluoRender (RRID:SCR_014303) Copy   

•   Source: SciCrunch Registry

https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release

Software package for multi-parametric model-fitting of 4D Magnetic Resonance Imaging data. Software library to facilitate voxel wise fitting on a number of datatypes including T1 and T2 relaxometry, Arterial Spin Labeled MRI, Diffusion Weighted Imaging and Dynamic Contrast Enhanced MRI. T

Proper citation: NiftyFit (RRID:SCR_014301) Copy   

•   Source: SciCrunch Registry

http://bioinfo.lifl.fr/RNA/sortmerna/

Sequence analysis software for filtering, mapping and OTU-picking NGS reads. SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SortMeRNA (RRID:SCR_014402) Copy   

•   Source: SciCrunch Registry

http://www.matrixscience.com/server.html

A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters.

Proper citation: Mascot (RRID:SCR_014322) Copy   

•   Source: SciCrunch Registry

http://www.openworm.org/

3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders.

Proper citation: OpenWorm (RRID:SCR_014650) Copy   

•   Source: SciCrunch Registry

http://darwin.uvigo.es/software/prottest_server.html

Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProtTest (RRID:SCR_014628) Copy   

•   Source: SciCrunch Registry