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https://github.com/ChristophRau/wMICA

Weighted implementation of Maximal Information Component Analysis, a co-expression network analysis algorithm for analysis of large interconnected networks and the identification of modules of similarly-acting nodes within the larger network.

Proper citation: wMICA (RRID:SCR_015490) Copy   

•   Source: SciCrunch Registry

http://www.re3data.org/

Global registry of research data repositories from all academic disciplines that allows the easy identification of appropriate research data repositories, both for data producers and users. Information icons display principal attributes of a repository that can be used for multi-faceted searches. Repository operators can suggest their infrastructures to be listed via a simple application form. A repository is indexed when the minimum requirements are met, i.e. mode of access to the data and repository, as well as the terms of use.

Proper citation: re3data.org (RRID:SCR_006782) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/phytools/index.html

Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species.

Proper citation: phytools (RRID:SCR_015502) Copy   

•   Source: SciCrunch Registry

https://library.ucsd.edu/research-and-collections/digital-collections/dams.html

A digital repository designed to store and manage digital assets of UC San Diego. The flexible architecture can accept a variety of data formats, schemas and web services when ingesting digital assets. It stores digital content files and allows for the creation, indexing and searching of associated metadata to locate and retrieve the content files. Content can be composed of files in any format, including text, sound, video, and images. The DAMS is also designed to facilitate the transfer and submission of the Library's digital assets to Chronopolis and the California Digital Library's Merritt, and can easily be extended to serve other purposes. Additionally, the DAMS is able to export data in many formats, including METS, HTML, OAI, RSS, CSV. Future plans include linking data sets with other universities and organizations. For more information about the DAMS, including the data model and technical diagram, see Github, https://github.com/ucsdlib: * DAMS Manual, https://github.com/ucsdlib/dams/wiki/DAMS-Manual * DAMS Hydra Head, https://github.com/ucsdlib/damspas * DAMS REST API, https://github.com/ucsdlib/dams/wiki/REST-API * DAMS Ontology, https://github.com/ucsdlib/dams/tree/master/ontology Additional information on Hydra is available at Project Hydra and Duraspace.

Proper citation: Digital Asset Management System (RRID:SCR_000491) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSCut

A software package for segmentation of structures using automated neual networks. This is the reference implementation using NAMIC software development best practices and the Insight Toolkit of the paper Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures. (PMID: 17904870). The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.

Proper citation: BRAINSCut (RRID:SCR_000861) Copy   

•   Source: SciCrunch Registry

http://aebruno.github.io/fusim/

A software tool for simulating fusion transcripts from a reference genome.

Proper citation: FUSIM (RRID:SCR_001015) Copy   

•   Source: SciCrunch Registry

http://force11.org/

A collaboration which works to transform scholarly communications through advanced use of computers and the Web. FORCE11 advocates the digital publishing of papers in order to enable more effective scholarly communication. The virtual community also advocates the publication of software tools and research communication by means of social media channels. As such, FORCE11 provides access to information and tools for the wider scientific community.

Proper citation: FORCE11 (RRID:SCR_005334) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/pilon/

Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.

Proper citation: Pilon (RRID:SCR_014731) Copy   

•   Source: SciCrunch Registry

http://neurosynth.org

Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image.

Proper citation: NeuroSynth (RRID:SCR_006798) Copy   

•   Source: SciCrunch Registry

https://github.com/NeuroimagingMetaAnalysis/ibma

Image-Based Meta-Analysis toolbox for SPM. Implementation of z-based statistics: Fisher's, Stouffer's.

Proper citation: IBMA toolbox (RRID:SCR_003772) Copy   

•   Source: SciCrunch Registry

http://omop.org/

Initiative to improve the safety of drugs on the market that utilized information drawn from patient medical record databases and health insurance claims to develop and test methods to detect and evaluate drug safety issues over time. The OMOP pilot project focused on the following objectives: * Defining and evaluating analytical methods that can be used to identify associations between drugs and health-related conditions. * Developing tools for organizing access to and evaluating the usefulness of multiple observational datasets. * Study how information from analyses of observational data can be used to inform ongoing pharmacovigilence efforts. The software tools - packaged as the OMOP Web RL Platform was developed and made available to the public, https://github.com/OMOP . In addition to these data tools, this collaborative research effort discovered methods for using data to reliably identify correlations between individual medical interventions and specific health outcomes. These insights are being used to help inform the FDA Sentinel Initiative as part of the Innovation in Medical Evidence Development and Surveillance (IMEDS) program. The achievements of the program include: * Establishment of a common data model and creation of data characterization tools, and vocabulary mappings * Implementation of Health Outcome of Interest definitions, including a program to implement these definitions as part of the Regularized Identification of Cohorts (RICO) * Release of 14 analysis methods to evaluate the performance of methods and data in identifying drug safety issues

Proper citation: Observational Medical Outcomes Partnership (RRID:SCR_003724) Copy   

•   Source: SciCrunch Registry

https://github.com/scidash/sciunit

A test-driven framework for formally validating scientific models against data.

Proper citation: SciUnit (RRID:SCR_014528) 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

https://github.com/Yandell-Lab/taxonomer_0.5

Genome sequence classification tool based on kmer. The code allows users to build nucleotide databases and protein databases, classify reads, construct binner databases, and create taxonomic relationship files. The website provides information on how to perform these actions with code, though users can access a web-based Taxonomer if they need/want to.

Proper citation: Taxonomer (RRID:SCR_014655) Copy   

•   Source: SciCrunch Registry

https://github.com/ebi-uniprot/ProtVista#annotations:r3_M7HqlEea7DSd1-qZqyw

A BioJS viewer for protein sequence features.

Proper citation: ProtVista (RRID:SCR_014623) Copy   

•   Source: SciCrunch Registry

http://bd2k.ini.usc.edu/tools/bdbag/

Software package with tools which assemble, identify, and provide access to subsets of data in a large and complex data collection workflow. The software utilities work primarily with BagIt packages that conform the BDDS Bagit and BDDS Bagit/RO profiles. JSON-LD is used to provide a standard way for linking metadata with existing ontologies and vocabularies.

Proper citation: Big Data Bag (RRID:SCR_014624) 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

http://stanfordnlp.github.io/CoreNLP/

A Java suite of core natural language analysis tools. It can take raw human language text input and give multiple outputs, including the base forms of words, their parts of speech, and marked up structure of sentences in terms of phrases or word dependencies. Supported languages include English, Arabic, Chinese, French, German, and Spanish.

Proper citation: Stanford CoreNLP (RRID:SCR_014778) Copy   

•   Source: SciCrunch Registry

http://microdraw.pasteur.fr/

Web application used to visualise and annotate collaboratively high resolution histology data. In short, it uses public ontologies to create collaborative, community-curated atlases. Annotations are vectorial, and users can use boolean operations to combine, subtract and split regions.

Proper citation: MicroDraw (RRID:SCR_014748) Copy   

•   Source: SciCrunch Registry

https://heal.nih.gov/

Project to help to end opioid addiction. Addiction Long-term Initiative or NIH HEAL Initiative, to speed scientific solutions to stem national opioid public health crisis. Initiative is funding hundreds of projects nationwide. Researchers are taking variety of approaches to tackle opioid epidemic through understanding, managing, and treating pain, and also through improving prevention and treatment for opioid misuse and addiction.

Proper citation: NIH Heal Project (RRID:SCR_022808) Copy   

•   Source: SciCrunch Registry