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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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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 | 2026-09-26 02:15:44 | 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 | 2026-09-26 02:15:44 | 0 | ||||||||||
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CATNAP Resource Report Resource Website 10+ mentions |
CATNAP (RRID:SCR_016170) | data analysis software, data processing software, software application, software resource | Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | database, analysis, | PMID:26044712 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016170 | SciCrunch Registry | CATNAP - Compile Analyze and Tally Neutralizing Antibody Panels | 2026-09-26 02:15:43 | 49 | |||||||||
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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 | 2026-09-26 02:15:44 | 1 | |||||
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L1000 Fireworks Display Resource Report Resource Website 10+ mentions |
L1000 Fireworks Display (RRID:SCR_016175) | L1000FWD | data processing software, data visualization software, software application, software resource, web application | Web application that provides interactive visualization of drug and small-molecule induced gene expression signatures. L1000FWD enables coloring of signatures by different attributes such as cell type, time point, concentration, as well as drug attributes such as MOA and clinical phase. | drug, small molecule, gene, expression, signature, moa, clinical, phase | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | PMID:29420694 | Freely available, Free, Available for download | SCR_016175 | SciCrunch Registry | L1000FWD: Large-scale Visualization of Drug-Induced Transcriptomic Signatures | 2026-09-26 02:15:43 | 16 | |||||||
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ObservableHQ Resource Report Resource Website 1+ mentions |
ObservableHQ (RRID:SCR_016173) | application programming interface, data access protocol, software resource, web application | Web application for a code and text writing environment. It uses javascript and can be used to produce executable papers. | code, text, environment, writing, paper, research, journal, execute, programming, javascript | Open source, Freely available, Account required, Account required for full access | SCR_016173 | SciCrunch Registry | 2026-09-26 02:15:43 | 7 | |||||||||||
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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 | 2026-09-26 02:15:44 | 1 | ||||||||
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GoldWave Resource Report Resource Website 50+ mentions |
GoldWave (RRID:SCR_016189) | data analysis software, data processing software, software application, software resource | Software that enables users to digitally edit audio files. GoldWave can record, edit, and analyze audio for research-related purposes. | audio, sound, analysis, acquisition, visualization, record, edit, analysis, auditory | Commercially available, Available for purchase | SCR_016189 | SciCrunch Registry | 2026-09-26 02:15:43 | 88 | |||||||||||
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Prucka CardioLab System Resource Report Resource Website |
Prucka CardioLab System (RRID:SCR_016180) | resource | Prucka CardioLab system delivers the EP data and visualization we need for electrophysiological study and catheter ablation. | hardware, instrument, equipment, cardiology, heart, electrophysiology, catheter, ablation | SCR_016180 | SciCrunch Registry | 2026-09-26 02:15:43 | 0 | ||||||||||||
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LINCS Joint Project - Breast Cancer Network Browser Resource Report Resource Website 1+ mentions |
LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) | LJP-BCNB, LJP, BCNB | data access protocol, service resource, software resource, web service | Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations. | breast, cancer, tissue, cluster, drug, perturbation, cell, line, gene, expression |
is related to: L1000 Characteristic Direction Signature Search Engine is related to: LINCS Project |
Breast cancer | NCI U54 CA189201; NHGRI U54 HG006093; NHLBI U54 HL127365; NHLBI U54 HL127624 |
PMID:29084964 | Free, Freely available | https://github.com/MaayanLab/LJP | SCR_016181 | SciCrunch Registry | LINCS Joint Project, Breast Cancer Network Browser | 2026-09-26 02:15:43 | 1 | ||||
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IHM-dictionary Resource Report Resource Website 1+ mentions |
IHM-dictionary (RRID:SCR_016186) | software resource | Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures. | macromolecule, mmcif, pdb, protein, database, databank, spectroscopy, microscopy, crystallography, proteomic | is related to: PDB-Dev | NSF DBI-1519158 | Free, Available for download | SCR_016186 | SciCrunch Registry | 2026-09-26 02:15:43 | 4 | |||||||||
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PDB-Dev Resource Report Resource Website 10+ mentions |
PDB-Dev (RRID:SCR_016185) | data repository, service resource, storage service resource | Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations. | protein, prototype, deposition, integration, hybrid, model, macromolecule, assembly, crystallography, spectroscopy, microscopy, |
is related to: IHM-dictionary has parent organization: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA |
NSF DBI-1519158 | Account required, Freely available, The research community can contribute to this resource | SCR_016185 | SciCrunch Registry | 2026-09-26 02:15:43 | 36 | |||||||||
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Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | analysis service resource, data analysis service, data management software, production service resource, service resource, software application, software resource | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | SciCrunch Registry | 2026-09-26 02:15:47 | 2 | |||||||
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Ximmer Resource Report Resource Website 1+ mentions |
Ximmer (RRID:SCR_016427) | data analysis software, data processing software, data visualization software, simulation software, software application, software resource | Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data. | cnv, copy, number, variant, exome, targeted, sequencing, data, next, generation, genomic | is listed by: OMICtools | Australian National Health and Medical Research Council ; National Eye Institute ; National Heart Lung and Blood Institute ; National Human Genome Research Institute ; Victorian State Government |
DOI:10.1101/260927 | Open source, Free, Available for download, Freely available | https://omictools.com/ximmer-tool, http://ximmer.org | SCR_016427 | SciCrunch Registry | 2026-09-26 02:15:46 | 4 | |||||||
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Canadian Open Neuroscience Platform Resource Report Resource Website 10+ mentions |
Canadian Open Neuroscience Platform (RRID:SCR_016433) | CONP | data or information resource, data repository, organization portal, portal, service resource, storage service resource | Web interface that facilitates open science for neuroscience community by simplifying global access to and sharing of datasets and tools. Portal internalizes typical data cycle of research project, beginning with data acquisition, followed by data processing with published tools, and ultimately publication of results with link to original dataset. Platform to form interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing. Provides unified interface to Canadian neuroscience research community. Open neuroscience research with sharing of both data and methods, to create large-scale databases, development of standards for sharing, facilitation of advanced analytic strategies, open dissemination to global community of neuroscience data and methods, and establishment of training programs for next generation of computational neuroscience researchers. | interactive, network, brain, research, interdisciplinary, student, training, international, partnership, clinical, translation, open, publishing, Canada |
is related to: Brain Canada is related to: Health Canada |
Open source | r3d100013461 | https://github.com/CONP-PCNO/conp-portal, https://doi.org/10.17616/R31NJMVP | SCR_016433 | SciCrunch Registry | CONP:Canadian Open Neuroscience Platform | 2026-09-26 02:15:47 | 11 | ||||||
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FFTW Resource Report Resource Website 10+ mentions |
FFTW (RRID:SCR_016554) | FFTW | software library, software resource, software toolkit | Software as a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). | library, collection, fast, C routine, compute, discrete, Fourier, transform | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | DOI:10.1109/JPROC.2004.840301 | Free, Available for download, Freely available | SCR_016554 | SciCrunch Registry | Fastest Fourier Transform in the West | 2026-09-26 02:15:48 | 17 | |||||||
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FCS Express Resource Report Resource Website 500+ mentions |
FCS Express (RRID:SCR_016431) | data analysis software, data processing software, software application, software resource | Software tool for flow and image cytometry data analysis by De Novo Software company. | flow, image, analysis, data, cytometry, De Novo Software, research, clinical, laboratory | is listed by: SoftCite | Commercially available, Tutorial available | SCR_016431 | SciCrunch Registry | 2026-09-26 02:15:47 | 518 | ||||||||||
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iMITS Resource Report Resource Website |
iMITS (RRID:SCR_016552) | iMITS | catalog, data or information resource, database | This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products. | international, tracking, system, mouse, production, data, store, catalog, phenotype, collection, mutation, molecular, structure, IKMC, IMPC |
is affiliated with: International Mouse Phenotyping Consortium (IMPC) is related to: GenTaR |
European Union 223592; NIH KOMP2 |
Restricted | SCR_016552 | SciCrunch Registry | international Micro Injection Tracking System | 2026-09-26 02:15:48 | 0 | |||||||
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Frozen Noise Resource Report Resource Website 1+ mentions |
Frozen Noise (RRID:SCR_016558) | data analysis software, data processing software, software application, software resource, software toolkit | Software analysis tools for electrophysiological somatosensory cortex databank. Allows to estimate the information content of spiking in single neuron resolution. It accompanies the open source intracellular recording database by Lantyer and colleagues. | electrophysiological, somatosensory, cortex, estimate, spiking, single, neuron, resolution | is related to: MATLAB | Free, Available for download, Freely available | SCR_016558 | SciCrunch Registry | 2026-09-26 02:15:48 | 4 | ||||||||||
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Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/, https://bio.tools/pavian | SCR_016679 | SciCrunch Registry | 2026-09-26 02:15:50 | 33 |
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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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