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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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Apache Spark Resource Report Resource Website 10+ mentions |
Apache Spark (RRID:SCR_016557) | data analytics software, data processing software, software application, software resource | Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework. | unified, analytics, engine, large, scale, data, processing |
is related to: VariantSpark is related to: spark-xml is related to: spark-xml-utils is related to: SparkFHE has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1145/2934664 | Free, Available for download, Freely available | SCR_016557 | SciCrunch Registry | 2026-11-07 12:01:39 | 43 | |||||||||
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docker4seq Resource Report Resource Website 1+ mentions |
docker4seq (RRID:SCR_017006) | data processing software, software application, software resource | Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers. | next, generation, sequencing, computing, application, read, mapping, count, docker, container, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: University of Turin;Turin;Italy |
Free, Available for download, Freely available | biotools:docker4seq | https://kendomaniac.github.io/docker4seq/index.html, https://bio.tools/docker4seq | SCR_017006 | SciCrunch Registry | 2026-11-07 12:01:37 | 6 | ||||||||
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AfterQC Resource Report Resource Website 10+ mentions |
AfterQC (RRID:SCR_016390) | data processing software, software application, software resource | Software that performs automatic filtering, trimming, error removing, and quality control for fastq data. | fastq, qc, editing, filtering, trimming, dna, rna, seq, sequence, sequencing, poly, pair-end, python | PMID:28361673 | Free, Available for download | SCR_016390 | SciCrunch Registry | After QC | 2026-11-07 12:01:39 | 15 | |||||||||
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Prophet Resource Report Resource Website 1+ mentions |
Prophet (RRID:SCR_017083) | data processing software, software application, software resource | Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton. | data, science, forecast, time, series, multiple, seasonality, linear, non linear, growth, analysis | is listed by: CRAN | DOI:10.7287/peerj.preprints.3190v2 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/prophet/, https://pypi.org/project/fbprophet/ | SCR_017083 | SciCrunch Registry | Prophet Automatic Forecasting Procedure | 2026-11-07 12:01:47 | 3 | |||||||
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Data Biosphere Resource Report Resource Website 1+ mentions |
Data Biosphere (RRID:SCR_016154) | data or information resource, portal, project portal | Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations. | data, environment, biomedicine, standard, module, community | Freely available | https://github.com/databiosphere/ | SCR_016154 | SciCrunch Registry | 2026-11-07 12:01:35 | 1 | ||||||||||
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WinRHIZO Resource Report Resource Website 10+ mentions |
WinRHIZO (RRID:SCR_017120) | data processing software, image analysis software, software application, software resource | Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots. | image, analysis, root, measurement, plant, morphology, topology, color, Regent Instruments Inc. | Available for purchase | SCR_017120 | SciCrunch Registry | 2026-11-07 12:01:37 | 16 | |||||||||||
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AIMLESS Resource Report Resource Website 500+ mentions |
AIMLESS (RRID:SCR_015747) | data processing software, software application, software resource | Data processing software for x-ray diffraction data. AIMLESS scales together multiple observations of reflections, and merges multiple observations into an average intensity. | xray, differentiation, observation, reflection, scaling, scale | has parent organization: MRC Laboratory of Molecular Biology | PMID:23793146 | Free, Available for download | SCR_015747 | SciCrunch Registry | 2026-11-07 12:01:30 | 571 | |||||||||
|
autoPROC Resource Report Resource Website 100+ mentions |
autoPROC (RRID:SCR_015748) | data processing software, software application, software resource, software toolkit | Data processing software for X-ray diffraction data. autoPROC is a set of tools and programs to automate steps involved in data processing, such as image analysis, integration, indexing, and determination. | xray, diffraction, data processing, crystallography | European Commission LSHG-CT-2003-503420 | PMID:21460447 | Free for academic use, Available for download | SCR_015748 | SciCrunch Registry | 2026-11-07 12:01:44 | 330 | |||||||||
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Science and Technology Facilities Council Resource Report Resource Website 1+ mentions |
Science and Technology Facilities Council (RRID:SCR_016713) | STFS | institution | One of nine Councils within United Kingdom Research and Innovation, an organisation that brings together the UK’s Research Councils, Innovate UK and Research England. Works in partnership with universities, research organisations, businesses, charities, and government to create the environment for research and innovation. | England, research, council, innovation, partnership, United Kingdom |
is parent organization of: CCP4 is parent organization of: CCP4 is parent organization of: Science and Technology Facilities Council Central Laser Facility OCTOPUS Microscopy Core Facility |
, GRID grid.14467.30, Wikidata Q1669366, Crossref Funder ID 501100000271, ISNI 0000 0001 2237 5485 | https://ror.org/057g20z61 | SCR_016713 | SciCrunch Registry | Science and Technology Facilities Council, STFC | 2026-11-07 12:01:32 | 2 | |||||||
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Stanford Center for Reproducible Neuroscience Resource Report Resource Website |
Stanford Center for Reproducible Neuroscience (RRID:SCR_016684) | data or information resource, organization portal, portal | Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects. | computing, tools, neuroscience, data, analyze, reproducibility, fMRI, OpenfMRI, OpenNeuro, Neurovault |
has parent organization: Stanford University; Stanford; California is parent organization of: OpenNeuro is parent organization of: OpenNeuro is parent organization of: NeuroVault |
SCR_016684 | SciCrunch Registry | 2026-11-07 12:01:36 | 0 | |||||||||||
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atacr Resource Report Resource Website 1+ mentions |
atacr (RRID:SCR_016286) | data processing software, software application, software resource | Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes. | normalization, bootstrap, bayes, factor, test, reference, design, seq, count, capture, data | Gatsby Charitable Foundation ; Marie Curie 656243 |
Free, Available for download, Tutorial available | SCR_016286 | SciCrunch Registry | 2026-11-07 12:01:31 | 2 | ||||||||||
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Studylog Resource Report Resource Website 1+ mentions |
Studylog (RRID:SCR_016682) | data or information resource, organization portal, portal, service resource | Commerciall organization to develop study protocols collaboratively to run and manage animal research studies for academic, government, biotech and pharmaceutical labs. Provides services, including product installation and configuration, user training, customization services and ongoing support. | develop, study, protocol, collaborative, animal, research | SCR_016682 | SciCrunch Registry | 2026-11-07 12:01:39 | 5 | ||||||||||||
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Slingshot Resource Report Resource Website 100+ mentions |
Slingshot (RRID:SCR_017012) | data processing software, software application, software resource | Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics. | identify, characterize, continuous, developmental, trajectory, single, cell, data, lineage, pseudotime, inference, transcriptomic | is used by: Totem | California Institute of Regenerative Medicine ; NCRR S10 RR029668; NHGRI T32 HG000047; NIA K01 AG045344; NIDCD R01 DC007235; NIMH U01 MH105979; Siebel Foundation |
PMID:29914354 | Free, Available for download, Freely available | SCR_017012 | SciCrunch Registry | 2026-11-07 12:01:33 | 102 | ||||||||
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imctools Resource Report Resource Website 10+ mentions Rating or validation data |
imctools (RRID:SCR_017132) | IMCtools | data processing software, software application, software resource | Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc. | preprocessing, pipeline, imaging, mass, cytometry, data, convert, IMC, raw, file, TIFF |
has parent organization: University of Zurich; Zurich; Switzerland is a plug in for: Fiji |
European Research Council ; NIDDK UC4 DK108132; PhosphonetPPM and MetastasiX SystemsX grant ; Roche Postdoctoral Fellowship ; SNSF Assistant Professorship grant ; Swiss National Science Foundation |
PMID:29605184 | Free, Available for download, Freely available | https://bodenmillergroup.github.io/imctools/build/html/index.html | SCR_017132 | SciCrunch Registry | imaging mass spectrometry tools | 2026-11-07 12:01:34 | 25 | |||||
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qMRLab Resource Report Resource Website |
qMRLab (RRID:SCR_016256) | data processing software, image analysis software, software application, software resource | Software for quantitative MR image analysis, simulation, and protocol optimization. It aims to provide the community with a tool for data fitting, plotting, simulation and protocol optimization for a variety of different quantitative models. | mr, image, analysis, simulation, optimize, protocol | Canadian Institute of Health Research (CIHR) ; Fonds de Recherche du Québec ‐ Nature et Technologies FRQNT 2015‐PR‐182754; Natural Sciences and Engineering Research Council of Canada (NSERC) ; Quebec Bio‐Imaging Network QBIN 8436‐0501 |
Open source, Free, Available for download | SCR_016256 | SciCrunch Registry | qMTLab, qMR Lab | 2026-11-07 12:01:45 | 0 | |||||||||
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NMF Toolbox Resource Report Resource Website 1+ mentions |
NMF Toolbox (RRID:SCR_017069) | data processing software, software application, software resource | Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach. | non negative, matrix, factorization, variant, coefficient, data, mining, bioinformatics |
is related to: MATLAB is related to: Algorithms and Framework for Nonnegative Matrix Factorization has parent organization: University of Southern California; Los Angeles; USA |
Free, Available for download, Freely available | https://sites.google.com/site/nmftool/, https://sail.usc.edu/~cvaz/nmftoolbox.html | SCR_017069 | SciCrunch Registry | NMF MATLAB Toolbox, Non-negative Matrix Factorization toolbox, Non negative Matrix Factorization Toolbox, NMF Toolbox | 2026-11-07 12:01:34 | 4 | ||||||||
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U.S. Culture Collection Network (USCCN) Resource Report Resource Website |
U.S. Culture Collection Network (USCCN) (RRID:SCR_016777) | USCCN | data or information resource, database, organization portal, portal | Research coordination network for ex situ Microbial Germplasm Collections to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of humankind by providing opportunities for US culture collection workers to engage with each other and with the broader culture collection community. | collection, microbial, germplasm, USA | U.S. National Science Foundation | SCR_016777 | SciCrunch Registry | US Culture Collection Network | 2026-11-07 12:01:33 | 0 | |||||||||
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Viagen Biotech Resource Report Resource Website 1+ mentions |
Viagen Biotech (RRID:SCR_017106) | material resource, reagent supplier | Commercial provider of innovative DNA extraction technologies and products for life science research. Reagents for preparation of DNA from mouse tails, ear pieces, yolk sac, and culture cells, DNA extracts, DNA markers. | Commercial, company, DNA, reagent, extraction, marker, biomedical | SCR_017106 | SciCrunch Registry | Viagen Biotech Inc. | 2026-11-07 12:01:40 | 1 | |||||||||||
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Object-Image Resource Report Resource Website 10+ mentions |
Object-Image (RRID:SCR_015720) | data processing software, image analysis software, software application, software resource | Image analysis software package that allows non-destructive image marking, input for further image processing, and marking the results of automatic measurements. Object-Image integrates measurements, macros, graphical objects and image names in a closed unit called 'object file' so that it reduces file clutter. | image marking, non-destructive, image analysis, text editor, debugging software | is related to: NIH Image | Free, Available for download, Runs on Mac OS | simon.bio.uva.nl/Object-Image/object-image.html | SCR_015720 | SciCrunch Registry | 2026-11-07 12:01:38 | 19 | |||||||||
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HMS LINCS Center Resource Report Resource Website 10+ mentions |
HMS LINCS Center (RRID:SCR_016370) | HMS LINCS | data or information resource, organization portal, portal | Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation. | LINCS, Program, library, network, cell, signature, analysis, drugs, human, research |
is related to: HMS LINCS Database has parent organization: Harvard Medical School; Massachusetts; USA |
NHLBI U54 HL127365 | PMID:29199020 | SCR_016370 | SciCrunch Registry | LINCS Center, Harvard Medical School LINCS Center, Harvard Medical School LINCS, Harvard Medical School (HMS) LINCS Center | 2026-11-07 12:01:45 | 15 |
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