Tools   Select Another Resource Report Type

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://manualzz.com/doc/6543996/drosophila-activity-monitoring-system-user-s-guide

Software tool used in Drosophila Activity Monitor system to scann data for errors. Also allows user to extract data from monitor files and bin data in different lengths.

Proper citation: Trikinetics DAM FileScan (RRID:SCR_021817) 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://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://www.mpi.nl/

Institute is entirely devoted to psycholinguistics – the study of how we produce and understand language, and how we acquire these skills as first or second language learners. The only institution in the world entirely dedicated to psycholinguistics, and is also one of only three among total of 90 within the Max Planck Society to be located outside Germany.

Proper citation: Max Planck Institute for Psycholinguistics; Nijmegen; Netherlands (RRID:SCR_021706) 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://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