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http://sourceforge.net/projects/cnv-webstore

Integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Platform to streamline processing and downstream interpretation of microarray data in clinical context. Analysis tools include CNV analysis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases.

Proper citation: CNV webstore (RRID:SCR_018007) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/microdynamix

Software tool for dendritic spine analysis that enables to visualize and quantify spine morphology over time. After loading image data acquired at different time points from in vivo and in vitro imaging sessions, automatically aligns images in 3D, then reconstructs dendritic branches, detects dendritic spines, and identifies important metrics such as length, thickness, and overall number, for accurate quantitative comparison.

Proper citation: MicroDynamix (RRID:SCR_017671) Copy   

•   Source: SciCrunch Registry

http://dichroweb.cryst.bbk.ac.uk/html/home.shtml

Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures.

Proper citation: DichroWeb (RRID:SCR_018125) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/covid-19

EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.

Proper citation: EMBL-EBI COVID-19 Portal (RRID:SCR_018337) Copy   

•   Source: SciCrunch Registry

https://viewer.cytosplore.org/

Web based interactive visual analysis system for exploration of single cell data published in Allen Cell Types Database and for number of single cell data resources of Brain Initiative Single Cell Network. Allows interactive exploration of hierarchies of cell types, visualization of transcriptome wide gene expression in combination with metadata of individual cells, performing differential analyses and statistics between manual selections of cells, or between pre-defined clusters throughout cellular hierarchy and more.

Proper citation: Cytosplore Viewer (RRID:SCR_018330) Copy   

•   Source: SciCrunch Registry

http://mole.upol.cz

Interactive web based tool for analyzing biomacromolecular channels, tunnels and pores. Enables two modes of calculation with one dedicated to analysis of channels and another for transmembrane pores. Can use PDB and mmCIF formats. Can analyze biomacromolecular structures stemming from NMR, X-ray and cryo-EM techniques. Interconnected with PDBe, CSA, ChannelsDB, OPM, UniProt to help setup and analysis of acquired results. Provides analytics for detection and structural characterization of channels and information about their physicochemical features.

Proper citation: MOLEonline (RRID:SCR_018314) Copy   

•   Source: SciCrunch Registry

https://pdc.cancer.gov/pdc/

Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication.

Proper citation: Proteomic Data Commons (RRID:SCR_018273) Copy   

•   Source: SciCrunch Registry

http://statistika.mfub.bg.ac.rs/interactive-repeated-experiments-dotplot/

Web tool for creating interactive graphics. Enables authors to create interactive graphics from data obtained with repeated independent experiments. Designed for laboratory studies with repeated experiments.

Proper citation: Interactive Repeated Experiments Dotplot (RRID:SCR_018328) Copy   

•   Source: SciCrunch Registry

https://www.bio.ifi.lmu.de/software/watchdog/index.html

Software workflow management system for automated and distributed analysis of large scale experimental data. Implemented in Java and is thus platform independent.

Proper citation: Watchdog (RRID:SCR_018355) Copy   

•   Source: SciCrunch Registry

https://github.com/embl-cba/fiji-plugin-bigDataProcessor/blob/master/README.md

Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy.

Proper citation: Big Data Processor (RRID:SCR_018484) Copy   

•   Source: SciCrunch Registry

https://www.perkinelmer.com/uk/product/harmony-4-8-office-hh17000001

Harmony high content imaging and analysis software. Used to quantify complex cellular phenotypes. Designed for PerkinElmer high content screening systems.

Proper citation: Harmony (RRID:SCR_018809) Copy   

•   Source: SciCrunch Registry

https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/

Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data.

Proper citation: RiboTaper (RRID:SCR_018880) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/StatClonotype/

Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences.

Proper citation: IMGT/StatClonotype (RRID:SCR_018963) Copy   

•   Source: SciCrunch Registry

https://github.com/auranic/ClinTrajan

Software Python package for analysis of trajectories in clinical datasets.

Proper citation: ClinTrajAn (RRID:SCR_019018) Copy   

•   Source: SciCrunch Registry

https://github.com/MRCIEU/TwoSampleMR

Software R package for performing Mendelian randomization using genome wide association study summary data.

Proper citation: TwoSampleMR (RRID:SCR_019010) Copy   

•   Source: SciCrunch Registry

http://tuskegee.eagle-i.net/i/00000136-648c-c32f-ee37-018280000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core provides services and training in computational biology, bioinformatics, experimental design and statistical analysis to the RCMI researchers and the biomedical research community at Tuskegee University.

Proper citation: Tuskegee University Computational Biology and Bioinformatics - Biomedical Information Management Services (RRID:SCR_010065) Copy   

•   Source: SciCrunch Registry

http://www.esri.com/software/arcgis/arcgis-for-desktop

Geographical information system software produced by Esri.

Proper citation: ArcGIS for Desktop Basic (RRID:SCR_011081) Copy   

•   Source: SciCrunch Registry

http://search.cpan.org/dist/ONTO-PERL/

ONTO-PERL is a collection of Perl modules to handle OBO-formatted ontologies (like the Gene Ontology). This code distribution gathers object-oriented modules (for dealing with ontology elements such as Term, Relationship and so forth), scripts (for typical tasks such as format conversions: obo2owl, owl2obo; besides, there are also many examples that can be easily adapted for specific applications), and a set of test files to ensure the suite''''s implementation quality. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: ONTO-PERL (RRID:SCR_005731) Copy   

•   Source: SciCrunch Registry

http://biodev.ece.ucsb.edu/projects/bisquik/wiki

A scalable web-based system for biological image analysis, management and exploration. The Bisque system incorporates many features useful to imaging researchers from image capture to extensible image analysis and querying. At the core, bisque maintains a flexible database of images and experimental metadata. Image analyses can be incorporated into the system and deployed on clusters and desktops. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content. New features and testing of Bisque version: 0.5.1, among many others are: # Parallel execution of datasets # Rich interfaces for autogenerated module UI # Abstracted storage system for local, irods, etc.. They are using Mercurial for their source control system. This should be installed before proceeding. Browse source on-line, http://biodev.ece.ucsb.edu/projects/bisquik/browser Bisque Installation, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/InstallationInstructions05 Bisque DOWNLOAD, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/download, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bisque (RRID:SCR_005564) Copy   

•   Source: SciCrunch Registry

http://lab.rockefeller.edu/chait/

Biomedical technology research center that develops cutting-edge mass spectrometric tools for analyzing peptides and proteins. It makes its software tools developed for data analysis freely available.

Proper citation: National Resource for the Mass Spectrometric Analysis of Biological Macromolecules (RRID:SCR_009007) Copy   

•   Source: SciCrunch Registry