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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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tidyverse Resource Report Resource Website 100+ mentions |
tidyverse (RRID:SCR_019186) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses. | data science, R package, data analysis, common data representation |
uses: ggplot2 uses: dplyr uses: tidyr is used by: tidySingleCellExperiment is used by: microViz is listed by: CRAN |
Free, Available for download, Freely available | https://www.tidyverse.org/, https://github.com/tidyverse/tidyverse | SCR_019186 | SciCrunch Registry | tidyverse 1.3.0 | 2026-11-07 11:59:16 | 259 | ||||||||
|
ObjectJ Resource Report Resource Website 10+ mentions |
ObjectJ (RRID:SCR_019190) | software resource | Software tool used for non destructive marking and linked results in ImageJ. Integrates image analysis across many images or stacks into single project file. | Image analysis file integration, file integration, image analysis, non destructive marking, ImageJ | is a plug in for: ImageJ | Free, Available for download, Freely available | SCR_019190 | SciCrunch Registry | 2026-11-07 11:59:21 | 30 | ||||||||||
|
Network-Based R-Statistics Resource Report Resource Website 1+ mentions |
Network-Based R-Statistics (RRID:SCR_019114) | NBR | data analysis software, data processing software, network analysis software, software application, software resource, software toolkit | Software tool as implementation of network based statistics toolbox in R. Includes mixed effects models. | Network based statistics, R, mixed effects model |
is listed by: CRAN is related to: Network Based Statistic Toolbox is related to: R Project for Statistical Computing |
Free, Freely available | SCR_019114 | SciCrunch Registry | 2026-11-07 11:59:10 | 3 | |||||||||
|
long-read-tools Resource Report Resource Website 10+ mentions |
long-read-tools (RRID:SCR_019116) | data or information resource, database, software repository, software resource | Interactive database of software tools for analysis of long read sequencing data.Catalogue of long-read sequencing data analysis tools. Catalogue of downstream analysis tools of real and synthetic long-read technologies. | Software tools collection, long read sequencing data, long read sequencing, data analysis, data analysis tools, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:32033565 | Free, Freely available | biotools:long-read-tools | https://github.com/shaniAmare/long_read_tools, https://bio.tools/long-read-tools | SCR_019116 | SciCrunch Registry | Long-Read-Tools, long-read-tools.org | 2026-11-07 11:59:05 | 14 | ||||||
|
Electron Microscopy Public Image Archive Resource Report Resource Website 50+ mentions |
Electron Microscopy Public Image Archive (RRID:SCR_019237) | EMPIAR | data or information resource, data repository, service resource, storage service resource | Public archive for raw electron microscopy image data. Resource for raw 2D electron microscopy images. Used to browse, upload and download raw images to build 3D structure. Provides access to raw data to facilitate methods development and validation. Complements Electron Microscopy Data Bank where 3D volumes are stored, and uses Aspera platform for data transfers. | CryoEM, cryo electron microscopy, raw electron microscopy images, electron microscopy images, raw images, raw data, image data | UK Biotechnology and Biological Sciences Research Council | PMID:27067018 | Free,Freely available | SCR_019237 | SciCrunch Registry | 2026-11-07 11:59:22 | 83 | ||||||||
|
runBioSimulations Resource Report Resource Website 1+ mentions |
runBioSimulations (RRID:SCR_019110) | software resource, web application | Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource. | Executing modeling studies, visualization, model reusing, simulation, bio.tools |
uses: BioSimulators is listed by: bio.tools is listed by: Debian |
Center for Reproducible Biomodeling Modeling ; National Institute of Bioimaging and Bioengineering ; National Institute of General Medical Sciences ; NIH ; NSF |
Free, Freely available | biotools:runbiosimulations | https://bio.tools/runbiosimulations | SCR_019110 | SciCrunch Registry | 2026-11-07 11:59:04 | 3 | |||||||
|
Phase Holographic Imaging: HoloMonitor live cell imaging and analysis system Resource Report Resource Website 1+ mentions |
Phase Holographic Imaging: HoloMonitor live cell imaging and analysis system (RRID:SCR_019231) | instrument resource | HoloMonitor live cell imaging and analysis system by Phase Holographic Imaging PHI AB. Contains small, digital live cell, quantitative phase imaging microscope HoloMonitor M4 designed to operate constantly inside incubator and HoloMonitor cell imaging software App Suite or Hstudio to continuously monitor and quantitatively analyze both individual cells and cell populations over time without any cellular labels or stains. Microscope can operate in cell incubator, hypoxia chamber or on lab bench. | Phase holographic imaging, microscope, instrument, equipment, phase imaging, incubator tolerant, hypoxia chamber tolerant, lab bench, digital holography, cell recording, live cell imaging, Phase Holographic Imaging PHI AB | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019231.pdf | https://phiab.com/ | SCR_019231 | SciCrunch Registry | , HoloMonitor microscope, HoloMonitor live cell imaging and analysis system, HoloMonitor® M4, HoloMonitor M3 | 2026-11-07 11:59:07 | 1 | |||||||||
|
BioSimulators Resource Report Resource Website 1+ mentions |
BioSimulators (RRID:SCR_019111) | software repository, software resource, web application | Web tool as collection of containerized biosimulation tools that provide consistent interfaces and guide to choosing simulator. Helps to find simulation tools that have capabilities, including supported modeling frameworks, simulation algorithms, and modeling formats, needed for specific modeling projects. | Containerized biosimulation tools, consistent interfaces, choosing simulator guide, supported modeling frameworks, simulation algorithms, modeling formats, bio.tools |
is used by: runBioSimulations is listed by: bio.tools is listed by: Debian |
Center for Reproducible Biomodeling Modeling ; National Institute of Bioimaging and Bioengineering ; National Institute of General Medical Sciences ; National Institutes of Health ; National Science Foundation |
Free, Freely available | biotools:biosimulators | https://bio.tools/biosimulators | SCR_019111 | SciCrunch Registry | 2026-11-07 11:59:20 | 5 | |||||||
|
AmpliconTagger Resource Report Resource Website 1+ mentions |
AmpliconTagger (RRID:SCR_019112) | data processing software, software application, software resource, workflow software | Software tool as rRNA marker gene amplicon pipeline coded in python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. Designed to work within HPC environment, supporting complex network of job dependencies with smart restart mechanism in case of job failure or parameter modifications. | High Performance Computing, HPC environment, rRNA gene amplicons, rRNA marker, gene amplicon pipeline, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:31816087 | Free, Freely available | SCR_019113, biotools:amplicontagger | https://bitbucket.org/jtremblay514/nrc_pipeline_public/src/master/, https://jtremblay.github.io/amplicontagger_guide.html, https://bio.tolols/amplicontagger | SCR_019112 | SciCrunch Registry | 2026-11-07 11:59:16 | 3 | |||||||
|
Elektra Academy Resource Report Resource Website |
Elektra Academy (RRID:SCR_019234) | data or information resource, training resource | Free curriculum, resources, and research for those considering incorporation of remote health monitoring. | Wearables, Electralabs, curriculum, resources, remote health monitoring, remote health monitoring incorporation, digital health, digital medicine | Restricted | SCR_019234 | SciCrunch Registry | 2026-11-07 11:59:18 | 0 | |||||||||||
|
Clinical Trials Viewer Resource Report Resource Website |
Clinical Trials Viewer (RRID:SCR_019230) | data access protocol, software resource, web service | Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set. | Drug, clinical data, clinical trial data, data, ClinicalTrials.gov data, FDA submission, FDA documents, FDA dataset |
is related to: ClinicalTrials.gov has parent organization: McGill University; Montreal; Canada |
Free, Available for download, Freely available | SCR_019230 | SciCrunch Registry | 2026-11-07 11:59:11 | 0 | ||||||||||
|
Program MARK Resource Report Resource Website 1+ mentions |
Program MARK (RRID:SCR_019281) | data analysis software, data processing software, software application, software resource | Software tool to provide parameter estimates from marked animals when they are re-encountered at later time, to create population size estimates. Used for analysis of data from marked individuals. | Parameter estimates, marked animal, marked animal data, re-encountered animals, population size estimates | has parent organization: Colorado State University; Colorado; USA | Free, Available for download, Freely available | SCR_019281 | SciCrunch Registry | 2026-11-07 11:59:08 | 4 | ||||||||||
|
Numbat Resource Report Resource Website 10+ mentions |
Numbat (RRID:SCR_019207) | data management software, software application, software resource | Software tool for managing extraction of large volumes of data from primary sources among multiple users, and then reconciling differences between them. Designed for use in systematic review projects in academic context. | Manage large references databases, large data, manage different extraction levels, multiple extraction forms, codebooks, reference network generation, publication database, systematic review, academic context | Free, Available for download, Freely available | https://github.com/bgcarlisle/Numbat, https://numbat.bgcarlisle.com | SCR_019207 | SciCrunch Registry | Numbat Systematic Review Manager | 2026-11-07 11:59:21 | 11 | |||||||||
|
Galactic Resource Report Resource Website |
Galactic (RRID:SCR_019208) | software resource, web application | Platform of Biorelate to all auto curated data captured from millions of textual articles. Galactic lets you build intuitive queries and explore results through different views that best suit your research needs.Used by pharmaceutical and biotech companies to explore auto curated knowledge from millions of text sources, revealing hidden insights that might otherwise be lost. | Auto curated data, textual articles, build intuitive queries, explore results, Biorelate Ltd. | Restricted | https://www.biorelate.com/products_and_services#galactic | SCR_019208 | SciCrunch Registry | Galactic AI | 2026-11-07 11:59:17 | 0 | |||||||||
|
variancePartition Resource Report Resource Website 50+ mentions |
variancePartition (RRID:SCR_019204) | data analysis software, data analytics software, data processing software, software application, software resource | Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays. | Repeated measures, variation in gene expression, RNA-seq datasets, high throughput genomic assays, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays, epigenomic sequencing assays, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: CRAN |
Icahn School of Medicine at Mount Sinai ; NHLBI U01 HL107388 |
PMID:27884101 | Free, Available for download, Freely available | biotools:variancepartition | https://bio.tools/variancepartition | SCR_019204 | SciCrunch Registry | 2026-11-07 11:59:17 | 62 | ||||||
|
BrainVision PyCorder Resource Report Resource Website 50+ mentions |
BrainVision PyCorder (RRID:SCR_019286) | data acquisition software, data processing software, software application, software resource | Open source acquisition program, based on Python programming language, for setting up BrainVision actiCHamp amplifier and storing data. | Acquision Python program, setting up actiCHamp amplifier, BrainVision | https://www.brainlatam.com/manufacturers/brain-products/pycorder-127 | SCR_019286 | SciCrunch Registry | PyCorder | 2026-11-07 11:59:12 | 55 | ||||||||||
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SIMR Resource Report Resource Website 1+ mentions |
SIMR (RRID:SCR_019287) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for power analysis of generalized linear mixed models by simulation. Used to calculate power for generalised linear mixed models. | Power analysis, generalized linear mixed models, calculate power, simulation | is listed by: CRAN | New Zealand Ministry of Business ; Innovation and Employment |
DOI:10.1111/2041-210X.12504 | Free, Available for download, Freely available | https://github.com/pitakakariki/simr | SCR_019287 | SciCrunch Registry | simr, simR | 2026-11-07 11:59:08 | 4 | ||||||
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MP3 tool Resource Report Resource Website 1+ mentions |
MP3 tool (RRID:SCR_019282) | simulation software, software application, software resource | Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathogenic proteins, pathogenic proteins prediction, genomic data, metagenomic data, partial pathogenic proteins, partial pathogenic proteins prediction, complete protein sequences, bio.tools |
is listed by: bio.tools is listed by: Debian |
Institutional Research Fund of IISER Bhopal | PMID:24736651 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mp3 | https://bio.tools/mp3 | SCR_019282 | SciCrunch Registry | MP3 | 2026-11-07 11:59:23 | 2 | |||||
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Expyfun Resource Report Resource Website 1+ mentions |
Expyfun (RRID:SCR_019285) | software library, software resource, software toolkit | Auditory and visual stimulus delivery library for psychoacoustics in Python. | Auditory, visual stimulus, stimulus delivery, library, psychoacoustics, Python. | Free, Available for download | SCR_019285 | SciCrunch Registry | 2026-11-07 11:59:18 | 1 | |||||||||||
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gbs2ploidy Resource Report Resource Website |
gbs2ploidy (RRID:SCR_019290) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package as functions for inference of ploidy from Genotyping By Sequencing data, including function to infer allelic ratios and allelic proportions in Bayesian framework. | Genotyping-by-sequencing data, GBS data, ploidy inference, allelic ratios infer, allelic proportions, Bayesian framework, ploidy level detection | is listed by: CRAN | PMID:28150424 | Free, Available for download, Freely available | SCR_019290 | SciCrunch Registry | 2026-11-07 11:59:24 | 0 |
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