Tools   Select Another Resource Report Type

https://github.com/Murali-group/SARS-CoV-2-network-analysis

Software tool to predict human proteins that interact with SARS-CoV-2 proteins and trace provenance of predictions.

Proper citation: SARS-CoV-2 network analysis (RRID:SCR_021811) Copy   

•   Source: SciCrunch Registry

https://hackaday.io/project/181604-mri-stereoscope

Project provides miniature mirror stereoscope system for MRI-scanner. System takes advantage of commonly used display equipment, MRI head coil, and display screen. Miniature Wheatstone stereoscope is used for human neuroimaging.

Proper citation: MRI-stereoscope project (RRID:SCR_021655) Copy   

•   Source: SciCrunch Registry

https://www.ibm.com/products/spss-statistics

Software package for statistics. Used to analyze and visualize data. Extensions can be used, Python and R programming language code, to integrate with open source software. Available for Windows and Mac operating systems.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago. Versions that were released after the acquisition would be given origin or publisher of IBM Corp. in Armonk, NY.

Proper citation: IBM SPSS Statistics (RRID:SCR_016479) Copy   

•   Source: SciCrunch Registry

https://www.mayo.edu/research/labs/tissue-repair-mechanobiology/software

Software tool to calculate 2D tractions exerted by adherent cell on its substrate. Used in field of mechanobiology to study contractile responses of variety of cell types.

Proper citation: TractionsForAll (RRID:SCR_021819) Copy   

•   Source: SciCrunch Registry

https://github.com/VisionandCognition/NHP-pycortex

Software tool as adaptation for NHP brains and pipelines. Pycortex python based toolkit for surface visualization of fMRI data.

Proper citation: NHP pycortex (RRID:SCR_021815) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/eqtl

Catalog provides uniformly processed gene expression and splicing QTLs from all available public studies on human. Expression and splicing QTLs recomputed from public datasets.

Proper citation: eQTL Catalogue (RRID:SCR_021700) Copy   

•   Source: SciCrunch Registry

https://github.com/jtamames/SqueezeMeta

Software tool as fully automated pipeline for metagenomic analysis. Used for metagenomics covering all steps of analysis. Features several characteristics including co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of abundances of genes in each metagenome. Includes binning and bin checking for retrieving individual genomes.

Proper citation: SqueezeMeta (RRID:SCR_021821) Copy   

•   Source: SciCrunch Registry

https://circexplorer2.readthedocs.io/en/latest/

Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs.

Proper citation: CIRCexplorer2 (RRID:SCR_021664) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/BASiCS/

Software tool for Bayesian analysis of single cell sequencing data. Used to perform statistical analyses of single cell RNA sequencing datasets in context of supervised experiments.

Proper citation: Bayesian Analysis of Single Cell Sequencing (RRID:SCR_021829) Copy   

•   Source: SciCrunch Registry

https://omgenomics.com/circa/

Software tool used to plot circular plots and visualize genomic data along genomic locations.

Proper citation: Circa (RRID:SCR_021828) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/ResourceWatch

Knowledgebase of biomedical research resources. Repository for storing validation and problematic information about variety of entities within biomedical domain, such as antibodies, cell lines, etc. Enables researchers to submit their own claims about specific entity to make validation/problematic information F.A.I.R. (Findable, Accessable, Interoperable, Reuseable).

Proper citation: Biomed Resource Watch (RRID:SCR_021761) Copy   

•   Source: SciCrunch Registry

https://rescognito.com/

Platform for recognizing and promoting Open Research. Open online service that aims to offer fairer and more democratic platform for recognizing researcher contributions.Allows researchers to openly acknowledge colleagues for meaningful contributions to research process, such as Publication, Mentoring,Teaching,Data sharing,Reproducibility practices, Sharing negative results, Participation in discussion groups,Software development, Clinical trials management, Leadership, Community outreach, Public engagement. ORCID iDs, DOIs, grant IDs and other persistent identifiers are used where available as links to appropriate contributions.

Proper citation: Rescognito (RRID:SCR_021874) Copy   

•   Source: SciCrunch Registry

https://sourcemd.toolforge.org/index_old.php

Web tool as prototype service to automatically generate Wikidata items using metadata from scholarly publications. Citation lookup tool in Wikipedia platform. Takes persistent identifier for scholarly article and processes it by importing bibliographic metadata into Wikidata items. In August 2018, it was merged with ORCIDator into single tool that allows for fully automated batch processing based on ISBN-13, DOI, ORCID iD, PubMed ID, PMCID identifiers.

Proper citation: SourceMD (RRID:SCR_021633) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/service.php?NetMHC-4.0

Web tool for binding prediction of peptides to MHC class I molecules. The newest version NetMHC- 4.0 is used for prediction of peptide MHC class I binding affinity using gapped sequence alignment that allows insertions and deletions in alignment.

Proper citation: NetMHC (RRID:SCR_021651) Copy   

•   Source: SciCrunch Registry

https://www.zeiss.com/microscopy/int/products/microscope-software/labscope.html

Software tool for image acquisition using WiFi-enabled Zeiss microscopes. Compatible with Windows PCs and with Apple tablets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Zeiss LabScope (RRID:SCR_021768) Copy   

•   Source: SciCrunch Registry

https://sites.cscc.unc.edu/aric/

Platform for prospective epidemiologic study conducted in four U.S. communities. One of most significant and longest running heart health studies and is the largest study of heart health in African Americans. ARIC investigates risk factors for heart disease and stroke, and connections between cardiovascular and cognitive health. ARIC includes two parts: Cohort Component and Community Surveillance Component. Cohort Component began in 1987, and each ARIC field center randomly selected and recruited cohort sample of individuals aged 45-64 from defined population in their community, to receive extensive examinations, including medical, social, and demographic data. In Community Surveillance Component, four communities are investigated to determine long term trends in hospitalized myocardial infarction and coronary heart disease deaths in men and women aged 35-84 years.

Proper citation: Atherosclerosis Risk in Communities (RRID:SCR_021769) Copy   

•   Source: SciCrunch Registry

https://paperswithcode.com/

Website devoted to papers that contain machine learning datasets, code, methods and evaluation tables. Done together with community, supported by NLP and ML.All content on this website is openly licenced under CC-BY-SA and everyone can contribute.Also operates specialized portals for papers with code in astronomy, physics, computer sciences, mathematics and statistics.

Proper citation: Papers with Code (RRID:SCR_021800) Copy   

•   Source: SciCrunch Registry

https://www.ionoptix.com/products/software/ionwizard-core-and-analysis/

Software tool to perform rapid fluorescence and morphometric real time, synchronous data acquisition with IonOptix systems, as well as polynomial fitting and analysis for myocyte research. Features include data trace averaging and filtering,composite images, and transient analysis. Integrates presentation of fluorescence traces and images, analog voltages, and cell length data under intuitive interface. Analyzes raw data by performing ratio, ion, or linear calibration calculations.

Proper citation: IonWizard (RRID:SCR_021764) Copy   

•   Source: SciCrunch Registry

https://cumulus.readthedocs.io/en/stable

Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.

Proper citation: Cumulus (RRID:SCR_021644) Copy   

•   Source: SciCrunch Registry

https://knowledge.figshare.com/plus

Web based interface designed for academic research data management and research data dissemination. Accepts all file types. Enables academics to upload, share, cite and discover all manner of research outputs with security of knowing our hosting options and platform support long term preservation of data.Used to share big datasets from 100GB up. Added features and expert guidance are also included for sharing your data FAIR-ly.During data deposit, personal email support is available and once submitted, Figshare data expert will conduct review of the metadata and spot check of your dataset files and offer guidance, with main aim of enhancing discoverability and reusability.

Proper citation: FigsharePlus (RRID:SCR_021762) Copy   

•   Source: SciCrunch Registry