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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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CycIF.org Resource Report Resource Website 10+ mentions |
CycIF.org (RRID:SCR_016267) | CycIF.org | data or information resource, experimental protocol, immuno detection protocol, immunofluorescence, narrative resource, web page | Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence. | immunofluorescence, cyclic, cycif, data, software, single cell, numeric, dataset, intratumoural, heterogeneity | has parent organization: LINCS Data Portal | NHLBI U54 HL127365 | PMID:26399630 | Public | SCR_016267 | SciCrunch Registry | cycif.org | 2026-11-07 11:58:34 | 16 | ||||||
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Fetal Actocardiograph MT-516 Resource Report Resource Website |
Fetal Actocardiograph MT-516 (RRID:SCR_016420) | data or information resource, portal, topical portal | Fetal actocardiograph instrument provided by TOITU CO., LTD. | instrument, fetal, actocardiogram, Toitu, obstetric, gynecology | Commercially available | SCR_016420 | SciCrunch Registry | 2026-11-07 11:58:16 | 0 | |||||||||||
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OMA Orthology database Resource Report Resource Website 1+ mentions |
OMA Orthology database (RRID:SCR_016425) | OMA | data access protocol, data or information resource, database, software application, software resource, standalone software, web service | Web based database interface for orthology prediction for the inference of orthologs among complete genomes. Used to relate genes across many species., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | interface, orthology, prediction, inference, complete, genome, species, data | Bayer Crop Science NV ; Swiss Institute of Bioinformatics ; UK Biotechnology and Biological Sciences Research Council ; University College London |
PMID:29106550 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016425 | SciCrunch Registry | Orthologous MAtrix | 2026-11-07 11:58:16 | 9 | |||||||
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kCSD-Matlab Resource Report Resource Website 1+ mentions |
kCSD-Matlab (RRID:SCR_016424) | kCSD | data analysis software, data processing software, software application, software resource | Software tool for analyzing recordings from multielectrodes. Source code for the Matlab implementation of the Kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes. | analyzing, recording, data, multielectrode, transmembrane, current, source, estimate, kernel, source, density, method | is related to: MATLAB | Free, Available for download, Freely available | SCR_016424 | SciCrunch Registry | kernel Current Source Density | 2026-11-07 11:58:41 | 3 | ||||||||
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Center for Expanded Data Annotation and Retrieval Resource Report Resource Website 1+ mentions |
Center for Expanded Data Annotation and Retrieval (RRID:SCR_016269) | CEDAR | controlled vocabulary, data or information resource, ontology, organization portal, portal | Develops information technologies that make authoring complete metadata more manageable. Its products aim to facilitate using the metadata in further research.Center to improve metadata and its use throughout biomedical sciences. Develops information technologies that make authoring complete metadata more manageable through better interfaces, terminology, metadata practices, and analytics. Optimizes metadata pathway from provider to end user. Provides way for funders to specify what metadata they want to collect as part of research life cycle. | Metadata, interface, metadata practice, analytics, metadata pathway, funded research, data repository, data collection, |
is related to: Stanford University; Stanford; California is related to: Yale University; Connecticut; USA is related to: University of Oxford; Oxford; United Kingdom has parent organization: Stanford Center for Biomedical Informatics Research is parent organization of: CEDAR Workbench |
NIAID U54 AI117925 | SCR_018150 | https://more.metadatacenter.org/ | SCR_016269 | SciCrunch Registry | 2026-11-07 11:58:13 | 4 | |||||||
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BIOQUANT Life Science Resource Report Resource Website 10+ mentions |
BIOQUANT Life Science (RRID:SCR_016423) | data analysis software, data processing software, image analysis software, software application, software resource, software toolkit | Software tool to collect and analyse data on images of tissue slides or welled plates.Supports high-throughput immunofluorescence and immunohistochemistry, stereology, densitometry, and 3D modeling. Used in bioscience research in animal models and human biopsy, developmental neuroscience, traumatic brain/spinal cord injury, glaucoma, eye-movement disorders, cardiovascular disease and muscle disorders. | BioQuant Inc., collect, analyse, data, tissue, slide, well, plate, capture, camera, scanned, image, immunofluorescence, immunohistochemistry, stereology, densitometry, 3D modeling | Commercially available, Tutoring available | SCR_016423 | SciCrunch Registry | 2026-11-07 11:58:36 | 20 | |||||||||||
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Illumina: MiSeqDx System Resource Report Resource Website 1+ mentions |
Illumina: MiSeqDx System (RRID:SCR_016380) | instrument resource | MiSeqDx System is FDA-regulated, CE-IVD-marked, NGS platform for in vitro diagnostic (IVD) testing. System offers both diagnostic and research modes. | Illumina, Sequencing System, Instrument Equipment, USEDit, | Restricted | SCR_020137, Model_Number_MiSeqDx | SCR_016380 | SciCrunch Registry | MiSeqDx | 2026-11-07 11:58:15 | 2 | |||||||||
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Illumina: HiSeq X Resource Report Resource Website 50+ mentions |
Illumina: HiSeq X (RRID:SCR_016385) | instrument resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15,2023. Sequencer for whole-genome sequencing. System consists of HiSeq X ultra-high-throughput instruments that deliver over 18,000 human genomes per year. | Illumina, Sequencing System, Instrument Equipment, USEDit, | THIS RESOURCE IS NO LONGER IN SERVICE | Model_Number_HiSeq X, SCR_020131 | https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet-hiseq-x-ten.pdf | SCR_016385 | SciCrunch Registry | HiSeq X | 2026-11-07 11:58:26 | 62 | ||||||||
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Illumina: HiSeq 2500 System Resource Report Resource Website 50+ mentions |
Illumina: HiSeq 2500 System (RRID:SCR_016383) | instrument resource | High-throughput sequencing system. High-quality data using proven Illumina SBS chemistry has made it the instrument of choice for major genome centers and research institutions throughout the world.HiSeq 2500 System has been discontinued. Illumina will support the instrument and intends to supply the reagents through February 28, 2023. | Illumina, Sequencing System, Instrument Equipment, USEDit, | works with: PySeq2500 | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_016383.pdf | SCR_020123, Model_Number_HiSeq 2500 | https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq2500/hiseq-2500-system-guide-15035786-03.pdf, https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq2500/hiseq-2500-system-guide-15035786-03.pdf | https://www.illumina.com/systems/sequencing-platforms/hiseq-2500.html | SCR_016383 | SciCrunch Registry | HiSeq 2500 | 2026-11-07 11:58:40 | 88 | ||||||
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PhenoSpD Resource Report Resource Website 1+ mentions |
PhenoSpD (RRID:SCR_016359) | PSD | data analysis software, data processing software, software application, software resource, software toolkit | Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool. | spectral, decomposition, matrice, phenotypic, correlation, estimation, multiple, testing, correction, human, phenome, genome, summary, statistic, decomposition, matrice, genomics |
is related to: University of Bristol; Bristol; United Kingdom is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016359 | SciCrunch Registry | Pheno Spectral Decomposition, PhenoSpD | 2026-11-07 11:58:35 | 6 | ||||||||
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Deeptools Resource Report Resource Website 1000+ mentions |
Deeptools (RRID:SCR_016366) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. | process, visualize, analysis, sequencing, data, ChIP-seq, RNA-seq, MNase-seq, quality, control, normalization, aligned, read, clustering, bioinformatic | works with: Galaxy | German Epigenome Programme DEEP 01KU1216G; German Research Foundation SFB 992 |
PMID:27079975 | Free, Available for download, Freely available | http://deeptools.ie-freiburg.mpg.de/ | SCR_016366 | SciCrunch Registry | 2026-11-07 11:58:35 | 2806 | |||||||
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SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | data analysis software, data processing software, software application, software resource, software toolkit | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | SciCrunch Registry | Statistical Meta Analysis for Gene EXPression | 2026-11-07 11:58:40 | 2 | |||||
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XLSTAT Resource Report Resource Website 100+ mentions |
XLSTAT (RRID:SCR_016299) | XLSTAT | data analysis software, data management software, data processing software, data visualization software, software application, software resource | Software for commercial data analysis and statistical software package for Microsoft Excel. | data, process, manage, analyze, visualize, graph, statistic, microsoft, excel | is related to: Microsoft Excel | Addinsoft | Commercially available, Trial available | SCR_016299 | SciCrunch Registry | XL STATistics | 2026-11-07 11:58:40 | 175 | |||||||
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TraCeR Resource Report Resource Website 10+ mentions |
TraCeR (RRID:SCR_016338) | data analysis software, data processing software, simulation software, software application, software resource, software toolkit | Software application for recovery of T cell receptor (TCR) data from single cell data. Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. | recovery, receptor, single, cell, data, computation, method, reconstruct, sequence, T lymphocyte, RNA, sequence |
is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is related to: European Bioinformatics Institute |
European Research Council ; the Lister Institute for Preventative Medicine (S.A.T.) |
PMID:26950746 | Free, Available for download, Freely available | SCR_016338 | SciCrunch Registry | 2026-11-07 11:58:40 | 14 | ||||||||
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migec Resource Report Resource Website 10+ mentions |
migec (RRID:SCR_016337) | MIGEC | data analysis software, data processing software, software application, software resource, software toolkit | Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires. | high sequencing, molecular, identifier, guided, error, correction, data, analysis, immune, recovery, T cell receptor, | European Regional Development Fund ; Molecular and Cell Biology program RAS ; Russian Foundation for Basic Research ; Russian President |
PMID:24793455 | Free, Available for download, Freely available | SCR_016337 | SciCrunch Registry | Molecular Identifier Guided Error Correction | 2026-11-07 11:58:35 | 11 | |||||||
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clustree Resource Report Resource Website 100+ mentions |
clustree (RRID:SCR_016293) | data analysis software, data processing software, data visualization software, software application, software resource | Software package which allows to produce clustering trees and visualize clusterings at different resolutions. Used in the analysis of large data sets to group together samples with similar properties. | clustering, tree, visualisation, data, set, group, sample, similar, property, different, resolution, cluster | is related to: R Project for Statistical Computing | Free, Freely available, Available for download | https://github.com/lazappi/clustree | SCR_016293 | SciCrunch Registry | 2026-11-07 11:58:14 | 100 | |||||||||
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NExT-EMA Resource Report Resource Website |
NExT-EMA (RRID:SCR_016291) | data analysis software, data processing software, software application, software resource | Software for combined elementary flux mode and network-embedded thermodynamic analysis. | efm, net, thermodynamics, flux, elementary, ema, stoichiometry | PMID:29237121 | Free, Available for download | SCR_016291 | SciCrunch Registry | 2026-11-07 11:58:40 | 0 | ||||||||||
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FluxModeCalculator Resource Report Resource Website 1+ mentions |
FluxModeCalculator (RRID:SCR_016290) | data analysis software, data processing software, software application, software resource | Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | efm, flux, stoichiometry, algorithm, matlab, linux, model, magnitude, bio.tools |
is listed by: Debian is listed by: bio.tools |
Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) ; CardioVascular Research Netherlands (CVON-ENERGISE) ; Center of Medical Systems Biology (CMSB) ; European Network for Genetic and Genomic Epidemiology (ENGAGE) ; Netherlands Consortium for Systems Biology (NCSB) |
PMID:26685305 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fluxmodecalculator, OMICS_10894 | https://bio.tools/fluxmodecalculator | SCR_016290 | SciCrunch Registry | Flux Mode Calculator | 2026-11-07 11:58:34 | 1 | |||||
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FLIR tools Resource Report Resource Website 10+ mentions |
FLIR tools (RRID:SCR_016330) | data analysis software, data processing software, image analysis software, software application, software resource | Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data. | thermography, FLIR Systems, image, data, measurement, analysis | Free, Available for download | SCR_016330 | SciCrunch Registry | 2026-11-07 11:58:40 | 16 | |||||||||||
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star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | alignment software, data processing software, image analysis software, software application, software resource | Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability. | hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environment | is related to: Systems Transcriptional Activity Reconstruction | AMEDD Advanced Medical Technology Initiative ; NHLBI U54 HL127624; NIGMS R01 GM126019 |
Free, Freely available, Available for download | https://github.com/paizhang/Hotstarting-For-STAR-Alignment | SCR_016294 | SciCrunch Registry | 2026-11-07 11:58:24 | 1 |
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