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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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mysamplesize Resource Report Resource Website 1+ mentions |
mysamplesize (RRID:SCR_017575) | software application, data processing software, data visualization software, data analysis software, software resource, portal, service resource, data or information resource | Software tool for experimental design, sample size determination and analysis by Tempest Technologies. | Experimental, design, sample, size, determination, analysis, Tempest Technologies |
is affiliated with: University of California at San Diego; California; USA is affiliated with: University of California at Davis; California; USA |
Restricted | SCR_017575 | MySampleSize | 2026-02-16 09:49:16 | 1 | |||||||||
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refgenie Resource Report Resource Website 1+ mentions |
refgenie (RRID:SCR_017574) | service resource, software application, software resource, data management software | Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis. | Organize, retrive, share, genome, analysis, reference, assembly, asset, manager, sequence, annotation, file, command, line, interface, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/698704 | Free, Available for download, Freely available | biotools:Refgenie | https://bio.tools/Refgenie | SCR_017574 | reference genome manager | 2026-02-16 09:49:16 | 6 | ||||||
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StatPackets Resource Report Resource Website |
StatPackets (RRID:SCR_017613) | data or information resource, standard specification, narrative resource | Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together. | Standardized, method, export, statistical, data, KOMP, result, analysis, together | is related to: Knockout Mouse Project | Free, Freely available | SCR_017613 | 2026-02-16 09:49:16 | 0 | ||||||||||
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Dynamo Resource Report Resource Website 1+ mentions |
Dynamo (RRID:SCR_017541) | software application, data processing software, data visualization software, data analysis software, image analysis software, software resource, image reconstruction software, 3d visualization software, time-series analysis software | Software tool for neuron timelapse reconstruction, registration and analysis for Dynamic Morphometrics. | Neuron, dynamic, morphometrics, timelapse, reconstruction, analysis, image | CIHR | Free, Available for download, Freely available | https://padster.github.io/pyDynamo/ | SCR_017541 | pyDynamo, python Dynamo | 2026-02-16 09:49:16 | 2 | ||||||||
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Transcriptive Resource Report Resource Website |
Transcriptive (RRID:SCR_017545) | software application, data processing software, software toolkit, data analysis software, software resource | Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results. | Analysis, pipeline, RNA, sequencing, data, raw, FastQ, input, align, read, gene, transcript, count, quality, control | Free, Available for download, Freely available | SCR_017545 | 2026-02-16 09:49:15 | 0 | |||||||||||
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QuB Resource Report Resource Website 1+ mentions |
QuB (RRID:SCR_018076) | QuB | software application, data processing software, software toolkit, data analysis software, software resource | Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Ion channel biophysics, neurophysiology data, hiddent state, memoryless system, solving kinetic model, data, Markov kinetics, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018076 | Quantify unknown Biophysics | 2026-02-16 09:49:25 | 2 | |||||||||
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MOON Resource Report Resource Website 1+ mentions |
MOON (RRID:SCR_018005) | software application, data processing software, software toolkit, data analysis software, software resource | Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid. | Diagnosis, rare disease, next generation sequencing, NGS, data, artificial intelligence, analysis, Diploid | Restricted | SCR_018005 | 2026-02-16 09:49:24 | 6 | |||||||||||
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SAVES Resource Report Resource Website 100+ mentions |
SAVES (RRID:SCR_018219) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web server for structure validation in homology modeling. Used to validate of obtained crude models. Structure analysis and validation server. | Structure validation, homology modeling, obtained model, analysis, validation server | has parent organization: University of California at Los Angeles; California; USA | Free, Freely available | SCR_018219 | SAVES v5.0, Structure Analysis and Verification Server | 2026-02-16 09:49:25 | 183 | |||||||||
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Gene Expression Profiling Interactive Analysis Resource Report Resource Website 5000+ mentions |
Gene Expression Profiling Interactive Analysis (RRID:SCR_018294) | GEPIA | web service, analysis service resource, data access protocol, software resource, production service resource, service resource | Web server for cancer and normal gene expression profiling and interactive analyses. Interactive web server for analyzing RNA sequencing expression data of tumors and normal samples from TCGA and GTEx projects, using standard processing pipeline. Provides customizable functions such as tumor or normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis. | Cancer gene expression, normal gene expression, analysis, RNA sequencing, expression data, TCGA project, GTEx project, patient survival analysis, correlation analysis |
is related to: Gene Expression Profiling Interactive Analysis 2 has parent organization: Peking University; Beijing; China |
Cancer | Peking University ; National Natural Science Foundation of China |
PMID:28407145 | Free, Freely available | SCR_018294 | 2026-02-16 09:49:26 | 5635 | ||||||
|
ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling. | Chromatin loop, CHi-C promoter, data, Hi-C visualization, interaction calling, data, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31118054 | Free, Freely available | biotools:ChiCMaxima | https://bio.tools/ChiCMaxima | SCR_018178 | 2026-02-16 09:49:27 | 2 | |||||||
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NeMO Analytics Resource Report Resource Website 10+ mentions |
NeMO Analytics (RRID:SCR_018164) | data analysis service, analysis service resource, topical portal, portal, production service resource, service resource, data or information resource | Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools. | Visualization, analysis, multi omic data, cell type, developing brain, adult brain, RNAseq, ATACseq, CHIPseq, fetal human prefrontal cortex, stem cell, neural induction, brain, data |
is used by: BICCN is related to: NeMOarchive is related to: BRAIN Initiative is related to: Brainome portal is related to: BRAIN Initiative Cell Atlas Network |
Free, Freely available | SCR_018244 | SCR_018164 | Neuroscience Multi-Omic Analytics | 2026-02-16 09:49:24 | 13 | ||||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NHLBI U54 HL127624; NIEHS P30 ES006096; NIMH R01 MH107487; NCI T32 CA236764; NCATS UL1 TR001425; NIGMS U01 GM120953 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-02-16 09:49:33 | 4 | ||||||||
|
TIMER Resource Report Resource Website 1000+ mentions |
TIMER (RRID:SCR_018737) | TIMER | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features. | Tumor, tumor infiltrating immune cell, immune cell, cell, analysis, cancer cell, cancer type, tumor immunological feature, tumor genomic feature, display | National Natural Science Foundation of China ; NCI CA180980; Dana-Farber Cancer Institute |
PMID:29092952 | Free, Freely available | SCR_018737 | Tumor IMmune Estimation Resource | 2026-02-16 09:49:31 | 2042 | |||||||
|
rVista Resource Report Resource Website 10+ mentions |
rVista (RRID:SCR_018707) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites. | Noncoding sequence, regulatory potential analysis, matrices search, TRANSFAC library collection, cis regulatory element, process alignment, zPicture, blastz, pairwise alignment, genome, analysis, transcription factor binding site, bio.tools |
is listed by: Debian is listed by: bio.tools works with: TRANSFAC |
PMID:15215384 | Free, Freely available | biotools:rvista | https://bio.tools/rvista | SCR_018707 | rVista 2.0 | 2026-02-16 09:49:33 | 30 | ||||||
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EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | software application, data processing software, software toolkit, data analysis software, software resource | Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. | Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools |
is listed by: Debian is listed by: bio.tools |
NICHD R01 HD068395; NIMH R21 MH112449; NICHD R21 HD075662; NIDA P30 DA027828; NIAID P30 AI050409; NIAID P30 AI027757; NICHD T32 HD007543 |
PMID:29731699 | Free, Available for download, Freely available | biotools:epimodel | https://bio.tools/epimodel | SCR_018539 | 2026-02-16 09:49:29 | 7 | ||||||
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QoRTs Resource Report Resource Website 10+ mentions |
QoRTs (RRID:SCR_018665) | software application, data processing software, software toolkit, data analysis software, software resource | Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R. | Quality control, data processing, RNAseq data, DNAseq data, analysis, data management, error detection, biases, artifacts, high throughput sequencing technology, | NHGRI | PMID:26187896 | Free, Freely available | https://github.com/hartleys/QoRTs | SCR_018665 | 2026-02-16 09:49:32 | 26 | ||||||||
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GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet https://bio.tools/GOnet |
SCR_018977 | 2026-02-16 09:49:37 | 3 | |||||||
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Genie 2000 Basic Resource Report Resource Website 1+ mentions |
Genie 2000 Basic (RRID:SCR_021933) | software application, data processing software, data analysis software, software resource, data acquisition software | Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data. | Data acquisition, display, analysis, gamma and alpha spectrometry data | Restricted | SCR_021933 | Genie 2000 Basic Spectroscopy Software, Marion Technologies Genie 2000 Basic Spectroscopy Software, Marion Technologies Genie 2000 Basic | 2026-02-16 09:50:08 | 2 | ||||||||||
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Internet Analysis Tools Registry Resource Report Resource Website 1+ mentions |
Internet Analysis Tools Registry (RRID:SCR_005638) | IATR | software application, data processing software, software repository, image analysis software, software resource | A centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools. It is hoped that this helps the tool developers to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development. This also helps tool users in identification of the existing tools for specific problems as they arise. The registry is designed to be self-moderated. This means that all tool entries are owned by some responsible party who enters the tool information, and keeps it up to date via the Web. | database, tool, neuroimaging, image, analysis |
lists: Extensible MATLAB Medical image Analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard Medical School; Massachusetts; USA |
Human Brain Project | Public Domain | nlx_146252 | SCR_005638 | IATR - Internet Analysis Tools Registry | 2026-02-16 09:46:40 | 1 | ||||||
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PRIMEGENS Resource Report Resource Website 1+ mentions |
PRIMEGENS (RRID:SCR_005474) | PRIMEGENS | data analysis service, analysis service resource, software resource, production service resource, service resource | A Web-based Tool for High-throughput Primer and Probe Design. The program has its different utilities available on its web server. A standalone version is also available. Algorithms: * SSPD - Sequence Specific Primer Design: to design primers for each of the specific sequences given by the user in the query input file against any alternate potential hybridization with any of the sequences given in the database input file. * PSPD - Probe Specific Primer Design: to design primers it selects the gene-specific fragments (probes) to design primer pairs for their PCR amplification. * FSPD Fragment Specific Primer Design: primer design algorithm used when there is a very long query sequence for which multiple primers are required for its amplification. * Check Binding Specificity * Probe Design Only: Probe design algorithm could be used to find sequence-specific probes, which doesn''t show any blast hit against database. Such probe design has been used for targeted sequencing like agilent sure-select technology with next-generation sequencing. | primer design, high-throughput primer, probe, microarray, analysis, blast, hybridization, primer, probe design, dna methylation |
is listed by: OMICtools has parent organization: University of Missouri; Missouri; USA |
DOE ; DOD ; NIH |
PMID:21415011 PMID:18579568 PMID:17951795 PMID:12424113 |
Free for academic use, Commercial use requires license | OMICS_00637, OMICS_02346 | http://digbio.missouri.edu/primegens/ | SCR_005474 | PRIMEGENS-w3, PRIMEGENS - High-throughput Primer and Probe Design, PRIMEGENSw3 | 2026-02-16 09:46:28 | 3 |
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