Tools   Select Another Resource Report Type

http://www.kitware.com/opensource/volview.html

A software for volume visualization that can be used by researchers to explore and analyze medical and scientific data. This software uses a variety of tools to load and visualize the data on either a 2D or 3D display. Theses tools include volume rendering, maximum intensity projections and oblique reformatting. Visualizations can be saved mid-session and be reopened at a later time.

Proper citation: VolView (RRID:SCR_014569) Copy   

•   Source: SciCrunch Registry

http://factominer.free.fr/index.html

Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables.

Proper citation: FactoMineR (RRID:SCR_014602) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.

Proper citation: FastQC (RRID:SCR_014583) Copy   

•   Source: SciCrunch Registry

http://www.plexon.com/products/omniplex-software

Neural data acquisition software for signal visualization in neuron recordings along with spike wave-form classification methods. It is made up of the PlexControl software program and the OmniPlex Server.

Proper citation: OmniPlex Software (RRID:SCR_014803) Copy   

•   Source: SciCrunch Registry

http://www.compudrug.com/metabolexpert

Software tool for initial estimation of the structural formula of metabolites, which might be formed by a substance in humans, animals or in plants. MetabolExpert is also capable of predicting the most common metabolic pathways in animals, exporting results to SDF and RDF format and graphical highlighting that empasizes the essence of metabolic reactions that occurred.

Proper citation: MetabolExpert (RRID:SCR_014908) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/bioinformatics/Pages/LaJolla_BioinformaticsandDataManagement.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 11132025. Facility that provides database development and management and bioinformatic network building services by utilizing on-site hardware and software. Three members of the facility are available to assist researchers with advanced bioinformatics and biostatistics analysis to help put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with the team statistician.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility (RRID:SCR_014868) Copy   

•   Source: SciCrunch Registry

http://www.leadscope.com

Commercial developer of database and predictive model software tools used in chemical toxicity assessment.

Proper citation: Leadscope (RRID:SCR_014904) Copy   

•   Source: SciCrunch Registry

http://netpyne.org/

Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks.

Proper citation: NetPyNE (RRID:SCR_014758) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.

Proper citation: Bowtie 2 (RRID:SCR_016368) Copy   

•   Source: SciCrunch Registry

https://aceabio.com/product/rtca-dp/

Data acquisition and analysis software used for xCELLigence Real Time Cell Analysis SP, DP and MP instruments. The software is used to program and execute experiments and analyze data.

Proper citation: RTCA Software (RRID:SCR_014821) Copy   

•   Source: SciCrunch Registry

http://www.biotech.uconn.edu/resources/biophysics

Software for analyzing sedimentation equilibrium (SE) data from analytical ultracentrifugation experiments. It uses a model-dependent simulation of data for matching data in order to determine when equilibrium has been achieved.

Proper citation: HeteroAnalysis (RRID:SCR_014991) Copy   

•   Source: SciCrunch Registry

https://proxl-ms.org/

Web application and database designed for sharing, visualizing, and analyzing protein cross-linking mass spectrometry data with emphasis on structural analysis and quality control. Includes public and private data sharing capabilities, project based interface designed to ensure security and facilitate collaboration among multiple researchers. Used for private collaboration and public data dissemination.

Proper citation: Protein Cross-Linking Database (RRID:SCR_021027) Copy   

•   Source: SciCrunch Registry

http://galaxyproject.org/

Open, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases.

Proper citation: Galaxy (RRID:SCR_006281) Copy   

•   Source: SciCrunch Registry

http://www.uni-koeln.de/med-fak/cgars/

Software package to dissect random from non-random patterns in copy number data and thereby to assess significantly enriched somatic copy number aberrations (SCNA) across a set of tumor specimens or cell lines.

Proper citation: CGARS (RRID:SCR_006404) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ubc.ca/ermineJ/

Data analysis software for gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are doing something interesting in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Major features include: * Implementation of multiple methods for gene set analysis: ** Over-representation analysis ** A resampling-based method that uses gene scores ** A rank-based method that uses gene scores ** A resampling-based method that uses correlation between gene expression profiles (a type of cluster-enrichment analysis). * Gene sets receive statistical scores (p-values), and multiple test correction is supported. * Support of the Gene Ontology terminology; users can choose which aspects to analyze. * User files use simple text formats. * Users can modify gene sets or create new ones. * The results can be visualized within the software. * It is simple to compare multiple analyses of the same data set with different settings. * User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results. * For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: ErmineJ (RRID:SCR_006450) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/ena/

Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.

Proper citation: European Nucleotide Archive (ENA) (RRID:SCR_006515) Copy   

•   Source: SciCrunch Registry

https://www.mdc-berlin.de/8551903/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep

Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data.

Proper citation: miRDeep (RRID:SCR_010829) Copy   

•   Source: SciCrunch Registry

https://www.metaboanalyst.ca/

Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification.

Proper citation: MetaboAnalyst (RRID:SCR_015539) Copy   

•   Source: SciCrunch Registry

https://CalRapp.org

A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates.

Proper citation: CalR (RRID:SCR_015849) Copy   

•   Source: SciCrunch Registry

https://www.biacore.com/lifesciences/service/downloads/software_licenses/biaevaluation/

Analysis software for life science data. This software package is for presentation and evaluation of sensorgram data from real-time BIA analyses.

Proper citation: BIAevaluation Software (RRID:SCR_015936) Copy   

•   Source: SciCrunch Registry