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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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Digital Expression Explorer 2 Project Resource Report Resource Website 1+ mentions |
Digital Expression Explorer 2 Project (RRID:SCR_016929) | DEE2 | data or information resource, data repository, database, portal, project portal, service resource, storage service resource | Software tool as a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive . DEE2 consists of three parts: Webserver where end-users can search for and obtain data-sets of interest, Pipeline that can download and process SRA data as well as users own fastq files, Back-end that collects, filters and organises data provided by contributing worker nodes. | transcriptome, database, RNA-seq, sequencing, processed, data |
is related to: Digital Expression Explorer 2 Source Code is related to: Digital Expression Explorer 2 Docker Image |
DOI:10.5281/zenodo.1561840 | Free, Freely available | SCR_016929 | SciCrunch Registry | DEE2 Project | 2026-09-26 02:15:52 | 4 | |||||||
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ALGGEN-PROMO Resource Report Resource Website 100+ mentions |
ALGGEN-PROMO (RRID:SCR_016926) | data analysis software, data or information resource, data processing software, laboratory portal, organization portal, portal, sequence analysis software, service resource, software application, software resource | Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches. | identify, transcription, factor, binding, site, DNA, sequence, species, regulatory, element, search | PMID:11847087 PMID:12824386 |
Free, Available for download, Freely available | SCR_016926 | SciCrunch Registry | PROMO, ALGorithmics and GENetics PROMO, ALGGEN, ALGGEN-PROMO | 2026-09-26 02:15:53 | 434 | |||||||||
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Comparative Metatranscriptomics Workflow Resource Report Resource Website 1+ mentions |
Comparative Metatranscriptomics Workflow (RRID:SCR_017109) | CoMW | data analysis software, data or information resource, data processing software, narrative resource, sequence analysis software, software application, software resource, training material, workflow | Software tool for standardized and validated workflow to functionally classify quality filtered mRNA reads from metatranscriptomic or total RNA studies generated using NGS short reads. Used for classification of these reads using assembled contigs to reference databases. | workflow, functionally, classify, mRNA, metatranscriptomic, RNA, next, generation, sequencing, NGS, short, read, assembly, contig, reference, database, bio.tools |
is listed by: bio.tools is listed by: Debian |
h2020 EU MicroArctic ITN | Free, Available for download, Freely available | biotools:comw | https://bio.tools/CoMW | SCR_017109 | SciCrunch Registry | 2026-09-26 02:15:54 | 3 | ||||||
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Scanco: Medical microCT 100 system Resource Report Resource Website 1+ mentions |
Scanco: Medical microCT 100 system (RRID:SCR_017119) | instrument resource | Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG. | SCANCO, micro, CT, computed, tomography, scanner, 3D, imaging, speciment, in vitro, analysis, visualization, image, data | Available for purchase | https://www.scanco.ch/images/Brochures/microct-v16.pdf | http://www.scanco.ch/en/systems-solutions/specimen/microct100.html | SCR_017119 | SciCrunch Registry | 2026-09-26 02:15:56 | 7 | |||||||||
|
CRISPR-P Resource Report Resource Website 10+ mentions |
CRISPR-P (RRID:SCR_016941) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment. | synthetic, single, RNA, CRISP, plant, Cas9, target, DNA, sequence, analysis, restriction, enzyme, sgRNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Fundamental Research Funds for the Central Universities ; National Basic Research Program of China ; Program for New Century Excellent Talents in University |
PMID:24719468 | Free, Freely available | biotools:CRISPR-P | https://bio.tools/CRISPR-P | SCR_016941 | SciCrunch Registry | CRISPR-P 2.0, Clustered Regularly Interspaced Short Palindromic Repeats P, CRISPR P | 2026-09-26 02:15:52 | 42 | |||||
|
MacroModel Resource Report Resource Website 100+ mentions |
MacroModel (RRID:SCR_016747) | simulation software, software application, software resource | Software package for molecular modeling. Computes free energy changes using free energy perturbation method. Used to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex. | molecular, modeling, free, energy, changes, perturbation, method, conformation, motion, interaction, ligand, receptor, complex | has parent organization: Schrodinger | Commercially available, Free version available | https://en.freedownloadmanager.org/Windows-PC/MacroModel.html | SCR_016747 | SciCrunch Registry | 2026-09-26 02:15:51 | 138 | |||||||||
|
ascat Resource Report Resource Website 10+ mentions |
ascat (RRID:SCR_016868) | ASCAT | data analysis software, data processing software, software application, software resource | Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data. | allele, specific, copy, number, analysis, tumor, purity, ploidy, sequencing, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:20837533 | Free, Available for download, Freely available | BioTools:ascat, biotools:ascat | https://github.com/VanLoo-lab/ascat, https://www.crick.ac.uk/research/labs/peter-van-loo/software, https://bio.tools/ascat, https://sources.debian.org/src/r-other-ascat/ | SCR_016868 | SciCrunch Registry | ASCAT 3.0, ASCAT 2.0, ASCAT 4.0, ASCAT 1.0, Allele-Specific Copy Number Analysis of Tumors, Allele Specific Copy Number Analysis of Tumors | 2026-09-26 02:15:51 | 42 | |||||
|
EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | data processing software, image processing software, software application, software resource | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | SciCrunch Registry | EMAN1, EMAN2 | 2026-09-26 02:15:51 | 107 | |||
|
Pyclone Resource Report Resource Website 10+ mentions |
Pyclone (RRID:SCR_016873) | data analysis software, data processing software, software application, software resource | Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing. | infer, prevalence, point, mutation, heterogeneous, cancer, probabilistic, population, NGS, sequencing, data, analysis | PMID:24633410 | Available for download, Free for academic, nonprofit use | https://bitbucket.org/aroth85/pyclone/wiki/Home | SCR_016873 | SciCrunch Registry | PyClone | 2026-09-26 02:15:51 | 46 | ||||||||
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Shape screening Resource Report Resource Website 1+ mentions |
Shape screening (RRID:SCR_016750) | simulation software, software application, software resource | Software tool for shape-based superposition and similarity searching. Identifies new compounds with shapes (and, if desired, other properties) that are similar to the known binder. | shape, based, superposition, search, new, compound | has parent organization: Schrodinger | Commercially available | SCR_016750 | SciCrunch Registry | 2026-09-26 02:15:52 | 3 | ||||||||||
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VORTEX Resource Report Resource Website 10+ mentions |
VORTEX (RRID:SCR_017047) | data analysis software, data processing software, software application, software resource | Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids. | single, cell, analysis, clustering, visualization, nonparametric, density, based, X shift | has parent organization: Stanford University; Stanford; California | PMID:27183440 | Free, Available for download, Freely available | http://web.stanford.edu/~samusik/vortex/ | SCR_017047 | SciCrunch Registry | VorteX Clustering Environment | 2026-09-26 02:15:55 | 19 | |||||||
|
Metab Resource Report Resource Website 1+ mentions |
Metab (RRID:SCR_016877) | Metab | data analysis software, data processing software, software application, software resource, software toolkit | Software package as a metabolomic data processing pipeline in R codes. | metabolomic, data, processing, pipeline, analysis, datasets | Health Research Council of New Zealand | DOI:10.1093/bioinformatics | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/Metab.html | SCR_016877 | SciCrunch Registry | Metabolome, Metab 1.0 | 2026-09-26 02:15:51 | 1 | ||||||
|
OpenBMI Resource Report Resource Website 1+ mentions |
OpenBMI (RRID:SCR_016876) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time. | brain, computer, interface, analysis, signal, acquire, filter, process, visualize, data | has parent organization: Korea University; Seoul; South Korea | Free, Available for download, Freely available | http://openbmi.org/ | SCR_016876 | SciCrunch Registry | 2026-09-26 02:15:53 | 5 | |||||||||
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BioNano: Irys system Resource Report Resource Website 10+ mentions |
BioNano: Irys system (RRID:SCR_016754) | instrument resource | System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies. | instrument, Irys, system, BioNano Genomics, BioNanomatrix, optical, next, generation, mapping, sequence, assembly, structural, variation, analysis, data, | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_016754.pdf | https://bionanogenomics.com/wp-content/uploads/2017/01/2016-Irys-System-Brochure.pdf | https://bionanogenomics.com/technology/genome-assembly/ | SCR_016754 | SciCrunch Registry | 2026-09-26 02:15:51 | 35 | ||||||||
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KnowEnG Resource Report Resource Website 1+ mentions |
KnowEnG (RRID:SCR_016875) | data or information resource, organization portal, portal, software resource, training resource | Part of the NIH Big Data to Knowledge (BD2K) Initiative. One of 11 Centers of Excellence in Big Data Computing. Platform for genomics data analysis where user-supplied data sets will be analyzed in the context of existing knowledge. E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data. | center, excellence, big, data, computing, biomedical, analytics |
has parent organization: Mayo Clinic has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIGMS U54 GM114838 | PMID:26205246 | https://github.com/BD2K/KnowEng | SCR_016875 | SciCrunch Registry | Knowledge Engine for Genomics, The Knowledge Engine for Genomics | 2026-09-26 02:15:51 | 1 | |||||||
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clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters. | data, statistical, analysis, visualization, gene, cluster, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
2007 Chang-Jiang Scholars Program ; Fundamental Research Funds for the Central Universities ; Guangdong Natural Science Research Grant ; National 973 Projects of China ; National Natural Science Foundation of China |
PMID:22455463 | Free, Available for download, Freely available | biotools:clusterprofiler | https://github.com/GuangchuangYu/clusterProfiler, https://guangchuangyu.github.io/software/clusterProfiler/, https://bio.tools/clusterprofiler | SCR_016884 | SciCrunch Registry | Cluster Profiler | 2026-09-26 02:15:52 | 13465 | |||||
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HaTSPiL Resource Report Resource Website 1+ mentions |
HaTSPiL (RRID:SCR_017059) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software Python tool for high throughput sequencing analysis, focused on high reliability, modularity and customisability. | next, generation, sequencing, pipeline, metadata, analysis, mutation, barcoding, customisability, modularity, bio.tools |
uses: Python Programming Language is listed by: Debian is listed by: bio.tools has parent organization: Italian Institute for Genomic Medicine; Turin; Italy |
Free, Available for download, Freely available | biotools:HatSPiL | https://bio.tools/HaTSPiL | SCR_017059 | SciCrunch Registry | 2026-09-26 02:15:54 | 1 | ||||||||
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BioPortainer Resource Report Resource Website 1+ mentions |
BioPortainer (RRID:SCR_017058) | data analysis software, data processing software, software application, software resource | Open source software designed in modular way, aimed at facilitating user interaction with Docker environments in three different computational layers like infrastructure, platform and application. | docker, bioportainer, user, interaction, docker, environment, infrastructure, platform, application | Free, Available for download, Freely available | https://github.com/BioPortainer/BioPortainer | SCR_017058 | SciCrunch Registry | BioPortainer Workbench | 2026-09-26 02:15:55 | 1 | |||||||||
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PRSice Resource Report Resource Website 100+ mentions |
PRSice (RRID:SCR_017057) | data analysis software, data processing software, software application, software resource | Software R package for calculating, applying, evaluating and plotting results of polygenic risk scores analysis. Performs simulation study to estimate P value significance threshold for high resolution PRS studies and produces plots for inspection of results. Operating Unix/Linux. | polygenic, risk, score, calculating, applying, plotting, result, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
EU ; NIHR Biomedical Research Centre |
PMID:25550326 | Free, Available for download, Freely available | OMICS_23656, biotools:prsice | https://choishingwan.github.io/PRSice/, https://bio.tools/prsice | SCR_017057 | SciCrunch Registry | prsice, PRSice-2, Polygenic Risk Score software, PRSice1, PRSice2 | 2026-09-26 02:15:54 | 110 | |||||
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CheckMyMetal Resource Report Resource Website 1+ mentions |
CheckMyMetal (RRID:SCR_016887) | CMM | data access protocol, software resource, web service | Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal. | metal, binging, site, validation, server, systematic, inspection, macromolecular, structure, ion, charge, position, atom | NHGRI HG008424; NIAID HHSN272201200026C; NIGMS GM117325 |
PMID:28291757 | Free, Freely available | SCR_016887 | SciCrunch Registry | 2026-09-26 02:15:52 | 8 |
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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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