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http://graphpad.com/

A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs.

Proper citation: GraphPad (RRID:SCR_000306) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.mdanderson.org/main/BreakFusion

Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data.

Proper citation: BreakFusion (RRID:SCR_001102) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/knime4bio/

A set of custom nodes for the KNIME (The Konstanz Information Miner) graphical workbench, for analysing next-generation sequencing (NGS) data without the requirement of programming skills.

Proper citation: Knime4Bio (RRID:SCR_005376) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/gap/

GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.

Proper citation: Genetic Analysis Package (RRID:SCR_003006) Copy   

•   Source: SciCrunch Registry

http://www.de-idata.com

A commercial organization that suppplies software which creates separate HIPAA-compliant repositories of de-identified patient records and reports. This software allows clinicians, researchers, and administrative leadership to safely access, search, share, and analyze de-identified patient-level data. DE-ID can be acquired as stand-alone tool or integrated with data networks or clinical information systems.

Proper citation: DE-ID Data Corp (RRID:SCR_008668) Copy   

•   Source: SciCrunch Registry

http://www.opentox.org/dev/apis/api-1.1/structure

Tools for the integration of data from various sources (public and confidential), for the generation and validation of computer models for toxic effects, libraries for the development and seamless integration of new algorithms, and scientifically sound validation routines. The goal of OpenTox is to develop an interoperable predictive toxicology framework which may be used as an enabling platform for the creation of predictive toxicology applications. OpenTox is relevent for users from a variety of research areas: Toxicological and chemical experts (e.g. risk assessors, drug designers, researchers) computer model developers and algorithm developers non specialists requiring access to Predictive Toxicology models and data OpenTox applications can combine multiple web services providing users access to distributed toxicological resources including data, computer models, validation and reporting. Applications are based on use cases that satisfy user needs in predictive toxicology. OpenTox was initiated as a collaborative project involving a combination of different enterprise, university and government research groups to design and build the initial OpenTox framework. Additionally numerous organizations with industry, regulatory or expert interests are active in providing guidance and direction. The goal is to expand OpenTox as a community project enabling additional expert and user participants to be involved in developments in as timely a manner as possible. To this end, our mission is to carry out developments in an open and transparent manner from the early days of the project, and to open up discussions and development to the global community at large, who may either participate in developments or provide user perspectives. Cooperation on data standards, data integration, ontologies, integration of algorithm predictions from different methods, and testing and validation all have significant collaboration opportunities and benefits for the community. OpenTox is working to meet the requirements of the REACH legislation using alternative testing methods to contribute to the reduction of animal experiments for toxicity testing. Relevant international authorities (e.g., ECB, ECVAM, US EPA, US FDA) and industry organizations participate actively in the advisory board of the OpenTox project and provide input for the continuing development of requirement definitions and standards for data, knowledge and model exchange. OpenTox actively supports the development and validation of in silico models and algorithms by improving the interoperability between individual systems (common standards for data and model exchange), increasing the reproducibility of in silico models (by providing a quality source of structures, toxicity data and algorithms) and by providing scientifically sound and easy-to-use validation routines. OpenTox is committed to the support and integration of alternative testing methods using in vitro assay approaches, systems biology, stem cell technology, and the mining and analysis of human epidemiological data. Hence the framework design must take into account extensibility to satisfy a broad range of scientific developments and use cases.

Proper citation: OpenTox Framework (RRID:SCR_008686) Copy   

•   Source: SciCrunch Registry

https://www.scanco.ch/microct100.html

Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG.

Proper citation: Scanco: Medical microCT 100 system (RRID:SCR_017119) Copy   

•   Source: SciCrunch Registry

https://biccn.org/data

Searchable table of datasets. Data generated from projects through BRAIN Initiative Cell Census Network. Datasets can be filtered by species, research investigator, grant number or experimental technique. Includes links to data directories at data archives and links to protocols.

Proper citation: BICCN Cell Registry (RRID:SCR_017267) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/home/strain

MGI integrates comparative data on inbred strain characteristics including SNPs, polymorphisms, and quantitative phenotypes.

Proper citation: Strains, SNPs and Polymorphisms (RRID:SCR_017518) Copy   

•   Source: SciCrunch Registry

http://promoter.bx.psu.edu/hi-c/

Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: 3D Genome (RRID:SCR_017525) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/pubmed/17539361

Study of twins and their families provides tool for disentangling genetic and environmental origins of traits. Study collected behavioral and psychopathological information using self-, parent and teacher reports, and focused on contributions of genetic and environmental risk factors to psychological health of young people.

Proper citation: Cardiff Study of all Wales and North West of England Twins (RRID:SCR_017480) Copy   

•   Source: SciCrunch Registry

https://www.medrxiv.org

Free online archive and distribution server for complete but unpublished manuscripts in the medical, clinical, and related health sciences. Preprints are preliminary reports of work that have not been certified by peer review. They should not be relied on to guide clinical practice or health related behavior and should not be reported in news media as established information. Research articles, systematic reviews and meta analyses, clinical research design protocols and data articles may be posted.

Proper citation: medRxiv (RRID:SCR_018222) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/

Repository of open source tools for behavioral neuroscience research. OpenBehavior features hardware (tools, devices, apparatuses), as well as software for data acquisition and analysis and for the investigation of animal behavior and cognition. Dedicated to accelerating research through promotion of collaboration and open source projects.

Proper citation: OpenBehavior (RRID:SCR_015938) Copy   

•   Source: SciCrunch Registry

http://imlspenticton.uzh.ch:3838/CATALYSTLite/

Software tool as interactive Shiny web application that provides user interface to mass cytometry data processing pipeline implemented in CATALYST R Bioconductor package.

Proper citation: CATALYSTLite (RRID:SCR_017126) Copy   

•   Source: SciCrunch Registry

http://connectivity.brain-map.org/transgenic

Data detailing transgene expression in Cre and other driver lines for adult and developing brain. Experiments include colorimetric in situ hybridization, fluorescent in situ hybridization and other histological methods. Expression maps of transgenic Cre and other driver lines in mice.

Proper citation: Allen Brain Atlas expression map of Cre and other drivers (RRID:SCR_017510) Copy   

•   Source: SciCrunch Registry

http://dsarm.niapublications.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 18, 2014.

A networking site for investigators using animal models to study aging, developed to provide a venue for sharing information about research models for aging studies. If you have tissue or data from animal models relevant to aging research that you are willing to share with other investigators, D-SARM allows you to identify the model and provides a secure, blinded email contact for investigators who would like to contact you about acquiring tissue or related resources. Investigators looking for resources from a particular model enter search terms describing the model of interest and then use the provided link to send emails to the contacts (names blinded) listed in the search results to initiate dialog about tissue or resources available for sharing. The database is housed on a secure server and admission to the network is moderated by the NIA Project Officer and limited to investigators at academic, government and non-profit research institutions. The goal is to provide a secure environment for sharing information about models used in aging research, promoting the sharing of resources, facilitating new research on aging in model systems, and increasing the return on the investment in research models.

Proper citation: Database for Sharing Aging Research Models (RRID:SCR_008691) Copy   

•   Source: SciCrunch Registry

https://nda.nih.gov/oai

Centralized, annotated repository for the Osteoarthritis Initiative (OAI) study, designed to accelerate research by organizing and linking extensive clinical, imaging (MRI/X-ray), and biomarker data. It aims to help researchers analyze knee osteoarthritis prevention, treatment, and progression.

Proper citation: OAI Knowledge base (RRID:SCR_028107) Copy   

•   Source: SciCrunch Registry

http://www.msbioworks.com/

A protein mass spectrometry service provider that delivers data to industrial and government organizations as well as academic institutions. Protein services include protein identification, mapping, profiling, and mass measurement. Post-translational modification services include PTM profiling, phospho-screening, and glyco-screening. Quantitative proteomics services include workflows for label free, TMT, SILAC, and PRM. MS Bioworks also provides immunoprecipitated protein analysis and custom analysis.

Proper citation: MS Bioworks (RRID:SCR_001043) Copy   

•   Source: SciCrunch Registry

http://www.duke.edu/web/gpcr-assay/index.html

Describes data from and access to permanent cell lines containing beta-arrestin fluorescent protein biosensors. This assay Bank provides plasmids, cells lines, and resulting data to the NIDA/NIH funded research community in order to better understand and combat addiction.

Proper citation: Addiction Research GPCR Assay Bank (RRID:SCR_002895) Copy   

•   Source: SciCrunch Registry

http://dash.harvard.edu/

Harvard University''s central service for sharing and preserving work. In addition to the scholarly journal articles targeted by Harvard''s several open access resolutions, DASH maybe used to self-archive manuscripts and materials. DASH supports a variety of file formats, and users are encouraged to deposit related materials with manuscripts (including data, images, audio and video files, etc.) When users deposit their work in DASH, it becomes visible to colleagues around the world by virtue of metadata harvesting, Google Scholar, and other indexing services. Higher visibility leads to higher rates of citation and impact. When users post early versions of their work, before publication, they establish intellectual priority sooner. Users act in their own best interests by taking part in the University''s mission to share and preserve the knowledge produced there. Because Harvard now has a prior, non-exclusive license to faculty journal articles in schools with open access policies, those faculty members are required to act accordingly when publishing journal articles, either by attaching an addendum to their publication agreement or obtaining a waiver. They then must deposit the publication in DASH.

Proper citation: Digital Access to Scholarship at Harvard (RRID:SCR_004122) Copy   

•   Source: SciCrunch Registry