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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-10-24 12:48:07 | 3 | |||||||
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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 | 2026-10-24 12:48:08 | 0 | |||||||||||
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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 | 2026-10-24 12:48:08 | 0 | ||||||||||
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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 | 2026-10-24 12:48:09 | 4 | ||||||||||
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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 | 2026-10-24 12:48:08 | 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 | 2026-10-24 12:48:08 | 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 | 2026-10-24 12:48:08 | 62 | ||||||
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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 | 2026-10-24 12:48:09 | 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 | 2026-10-24 12:48:09 | 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 | 2026-10-24 12:48:09 | 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 | 2026-10-24 12:48:09 | 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 | 2026-10-24 12:48:09 | 0 | |||||||||
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BayesEpiModels Web App Resource Report Resource Website 1+ mentions |
BayesEpiModels Web App (RRID:SCR_019292) | analysis service resource, production service resource, service resource, software resource, web application | Web app to help assess both short- and long-term forecasts of COVID-19 across the United States at multiple levels. Done by implementing one time-series model (ARIMA), one compartmental models (basic SIR), and six classical growth models, which all yield satisfactory prediction results in the past and current pandemics at early stage. | COVID-19, SARS-CoV-2, stochastic growth model, stochastic SIR model, Bayesian inference, | Free, Freely available | SCR_019292 | SciCrunch Registry | 2026-10-24 12:48:09 | 1 | |||||||||||
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ChiRA Resource Report Resource Website 1+ mentions |
ChiRA (RRID:SCR_019219) | data or information resource, data processing software, narrative resource, software application, software resource, software toolkit, training material, workflow | Software tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. | RNA-RNA interactome experimental data, experimental data analysis, miRNA, RNA-RNA interactome, RNA structurome, CLASH, CLEAR-CLIP, PARIS, SPLASH, chimeric read, read, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:chira | https://rna.usegalaxy.eu/, https://bio.tools/chira | SCR_019219 | SciCrunch Registry | Chimeric Read Analyzer | 2026-10-24 12:48:08 | 6 | |||||||
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ConPlot Resource Report Resource Website 1+ mentions |
ConPlot (RRID:SCR_019216) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web application for visualisation of information derived from residue contact predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.Provides interactive interface for researchers in field of protein bioinformatics that are interested in analysing data on given protein. | Residue contact predictions, protein, secondary structure predictions, transmembrane helical topology, sequence conservation, protein bioinformatics, analysing data |
is related to: CCP4 has parent organization: University of Liverpool; Liverpool; United Kingdom |
Restricted | SCR_019216 | SciCrunch Registry | 2026-10-24 12:48:08 | 2 | ||||||||||
|
Trial Registration Number screener Resource Report Resource Website 1+ mentions |
Trial Registration Number screener (RRID:SCR_019211) | TRNscreener | data analysis software, data processing software, software application, software resource | Software tool as R script to provide function that takes two arguments: path to folder of plain text files named by their DOI, and output filename. For each file in folder, it searches for trial identifiers based on regex matching and writes CSV that contains all trial registration numbers and in case of ClinicalTrials.gov entries, whether they correspond to registry entry on ClinicalTrials.gov. | ClinicalTrials.gov, plain text files, DOI named, output filename, trial identifiers searches, regex matching, trial registration numbers, ASWG | has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany | Free, Available for download, Freely available | SCR_019211 | SciCrunch Registry | Trial Registration Number screener, Trial registration number screener | 2026-10-24 12:48:08 | 1 | ||||||||
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spdep Resource Report Resource Website 1+ mentions |
spdep (RRID:SCR_019294) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package as collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree. | Spatial weights matrix objects, spatial dependence, weighting schemes, spatial weights, matrix objects | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/r-spatial/spdep/ | SCR_019294 | SciCrunch Registry | Spatial Dependence: Weighting Schemes and Statistics, spatial dependence | 2026-10-24 12:48:09 | 2 | ||||||||
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scales Resource Report Resource Website 10+ mentions |
scales (RRID:SCR_019295) | data processing software, data visualization software, software application, software resource, software toolkit | Software R package as scale functions for visualization. Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends. | Scale functions, visualization, graphical scales, map data, axes, determining breaks, legend, determining labels | Free, Available for download, Freely available | https://github.com/r-lib/scales | SCR_019295 | SciCrunch Registry | 2026-10-24 12:48:09 | 18 | ||||||||||
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Agilent: 1290 Infinity II Online SPE System Resource Report Resource Website |
Agilent: 1290 Infinity II Online SPE System (RRID:SCR_019380) | instrument resource | Online SPE System automates solid phase extraction to enrich analytes, remove matrix components or lower detection limits. | Agilent, GPS/SEC System, Instrument Equipment, USEDit, | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019380.pdf | Model_Number_1290 Infinity II Online SPE | SCR_019380 | SciCrunch Registry | 2026-10-24 12:48:11 | 0 | |||||||||
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Agilent: 240Z AA Atomic Absorption System Resource Report Resource Website |
Agilent: 240Z AA Atomic Absorption System (RRID:SCR_019385) | instrument resource | Atomic Absorption System is used for detection limits and analyzes difficult matrices. | Agilent, Atomic Absorption System, Instrument Equipment, USEDit, | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019385.pdf | Model_Number_240Z_AA | SCR_019385 | SciCrunch Registry | 2026-10-24 12:48:11 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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