Tools   Select Another Resource Report Type

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://archive.mpi.nl/tla/elan

Software annotation tool for audio and video recordings. Annotation can be sentence, word or gloss, comment, translation or description of any feature observed in media. Annotations can be created on multiple layers. Tiers can be hierarchically interconnected. Annotation can either be time-aligned to media or it can refer to other existing annotations. Content of annotations consists of Unicode text and annotation documents are stored in XML format (EAF).

Proper citation: ELAN (RRID:SCR_021705) Copy   

•   Source: SciCrunch Registry

http://www.psychencode.org/

Collaboration between research institutes working to provide framework of regulatory genomic elements in individuals with neuropsychiatric disorders.Collaboration has resulted in comprehensive set of manuscripts published in Science providing new insights into biology of developing, adult, and diseased human brain.Manuscripts are organized around three flagship articles, first analyzing human development, second studying disease transcriptomes, and third integrating tissue and single cell data with deep learning approaches.

Proper citation: PsychENCODE (RRID:SCR_021760) 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://github.com/igordot/sns

Set of automated workflows for common sequencing based (Illumina) protocols, such as RNA-seq, ChIP-seq, ATAC-seq, WGBS/RRBS methylation, whole genome/exome/targeted variant detection, and contaminant screening. Sequencing data analysis pipelines.

Proper citation: Seq-N-Slide (RRID:SCR_021752) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/dries_decap/halvadeforspark/

Software implements germline and somatic variant calling pipelines based on best practices pipelines from Broad Institute using Spark framework. Produces VCF output file which contains single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) when supported by used tools. Program requires Spark on either local cluster with one or more nodes, Amazon EMR cluster or Docker image to run.

Proper citation: Halvade Somatic (RRID:SCR_021771) Copy   

•   Source: SciCrunch Registry

http://justusrandolph.net/kappa/

Software tool can be used to calculate kappa, chance adjusted measure of agreement, for any number of cases, categories, or raters.

Proper citation: Online Kappa Calculator (RRID:SCR_021770) 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://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

https://www.trikinetics.com/Downloads/DAMSystem3%20Software%20Data%20Sheet.pdf

Software tool for data collection to upload output from set of activity monitors and periodically saves it in disk files on Macintosh or Windows PC. Part of TriKinetics Drosophila Activity Monitoring System.

Proper citation: TriKinetics DAMSystem3 Software (RRID:SCR_021809) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16039

Browser for mouse developmental anatomy. Ontology of mouse developmental anatomy was originally developed by Jonathan Bard and his colleagues as part of Edinburgh Mouse Atlas Project (EMAP) in order to provide structured controlled vocabulary of stage specific anatomical structures for developing laboratory mouse.

Proper citation: Mouse Developmental Anatomy Ontology Browser (RRID:SCR_021808) Copy   

•   Source: SciCrunch Registry

https://github.com/jeffdaily/parasail

Software tool as multiple sequence alignement for global, local and semi global alignments.

Proper citation: PARASAIL (RRID:SCR_021805) Copy   

•   Source: SciCrunch Registry

http://www.lbgi.fr/~julie/LEON-BIS

Software tool for sequence alignments evaluation. Multiple alignment evaluation of sequence neighbours using Bayesian inference system. Used to distinguish sections in multiple sequence alignments that are conserved across whole family or within subfamilies, and should be useful for automatic, high-throughput genome annotations, 2D/3D structure predictions, protein-protein interaction predictions etc.

Proper citation: LEON BIS (RRID:SCR_021803) Copy   

•   Source: SciCrunch Registry

https://training.incf.org

Portal that provides multimedia educational content from courses, conference lectures, and laboratory exercises from some of leading neuroscience institutes and societies to be more accessible to global neuroscience community.

Proper citation: TrainingSpace (RRID:SCR_022036) Copy   

•   Source: SciCrunch Registry

https://www.cellscale.com/products/microtester/

System includes MicroTester G2 device and software. MicroTester G2 is mechanical test device that can be used to test properties of variety of tissues and materials. Main components of device are load application microbeam, actuators, imaging system, and fluid bath/test chamber. MicroTester G2 software is divided into two modules: data collection module and review and analysis module.

Proper citation: CellScale: MicroTester G2 system (RRID:SCR_022034) Copy   

•   Source: SciCrunch Registry

http://www.ssu.ac.ir

Public university located in center of Iran in World Heritage city of Yazd.

Proper citation: Shahid Sadoughi University of Medical Sciences; Yazd; Iran (RRID:SCR_022031) Copy   

•   Source: SciCrunch Registry