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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Indiana University Center for Genomics and Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
Indiana University Center for Genomics and Bioinformatics Core Facility (RRID:SCR_017165) | CGB | access service resource, core facility, data or information resource, service resource | CGB offers range of genomic services, including high-throughput DNA/RNA extraction, library preparation, next-generation sequencing, and bioinformatic analysis. | ABRF, genomic services, DNA/RNA extraction, library preparation, next-generation sequencing, bioinformatic analysis, |
is listed by: ABRF CoreMarketplace has parent organization: Indiana University Bloomington; Indiana; USA |
Restricted | SCR_025534, ABRF_2841 | https://indianactsi.org/servicecores/core/20/, https://coremarketplace.org/?FacilityID=2841&citation=1 | SCR_017165 | SciCrunch Registry | Indiana University Bloomington Center for Genomics and Bioinformatics | 2026-09-26 02:17:15 | 3 | ||||||
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NCBI Virus Resource Report Resource Website 50+ mentions |
NCBI Virus (RRID:SCR_018253) | data access protocol, data or information resource, portal, software resource, topical portal, web service | Community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories. Integrative, value added resource designed to support retrieval, display and analysis of curated collection of virus sequences and large sequence datasets. Used to increase usability of data archived in GenBank and other NCBI repositories. | Viral sequence data, viral data retrival, viral data analysis, viral data display, curated virus sequence, data set |
is related to: RefSeq is related to: GenBank |
PMID:27899678 | Free, Freely available | SCR_018253 | SciCrunch Registry | National Center for Biotechnology Information Virus | 2026-09-26 02:17:16 | 76 | ||||||||
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NEB Tm calculator Resource Report Resource Website 1+ mentions |
NEB Tm calculator (RRID:SCR_017969) | data access protocol, service resource, software resource, web service | Calculator to estimate appropriate annealing temperature when using NEB PCR products.Tm calculator provided by New England Biolabs. | Calculate, estimate, annealing, temperature, PCR, product, New England Biolabs Inc., NEBtool | SCR_017969 | SciCrunch Registry | 2026-09-26 02:17:15 | 3 | ||||||||||||
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PASC Resource Report Resource Website 1+ mentions |
PASC (RRID:SCR_016642) | PASC | analysis service resource, data access protocol, data or information resource, database, production service resource, service resource, software resource, web service | Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. | analysis, pairwise, identity, distribution, viral, family, sequence, classification, data, taxonomy | has parent organization: NCBI | National Library of Medicine | PMID:25119676 | Free, Public | SCR_016642 | SciCrunch Registry | PAirwise Sequence Comparison | 2026-09-26 02:17:14 | 6 | ||||||
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3DOC Resource Report Resource Website |
3DOC (RRID:SCR_021547) | data or information resource, instrument resource, portal, project portal | Project related to animals learned perform action in order to achieve reward. Fully 3D printable chamber able to perform operant conditioning using off-the-shelf, low-cost optical and electronic components, that can be reproduced rigorously in any laboratory equipped with 3D printer. | Instrument, operant conditioning, 3D printable chamber, OpenBehavior | is listed by: OpenBehavior | DOI:10.1523/eneuro.0502-19.2020 | Commercially available | SCR_021547 | SciCrunch Registry | 2026-09-26 02:17:17 | 0 | |||||||||
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CMMT Mouse Animal Production Service Resource Report Resource Website |
CMMT Mouse Animal Production Service (RRID:SCR_016403) | EMS, MAPS, CMMT MAPS, CMMT EMS | biomaterial supply resource, material resource, organism supplier | Supplier of mice for research purposes. The service is run by Dr. Elizabeth M. Simpson, Ph.D. and is affiliated with her lab. | mouse, strain, supply, research, repository, subject, genetic engineering, knockout, mice, gene, model | SCR_016403 | SciCrunch Registry | Mouse Animal Production Service (MAPS), Centre for Molecular Medicine and Therapeutics MAPS, Dr. Elizabeth M. Simpson PhD, Elizabeth M. Simpson, Mouse Animal Production Service, Centre for Molecular Medicine and Therapeutics Mouse Animal Production Service | 2026-09-26 02:17:14 | 0 | ||||||||||
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SNP2TFBS Resource Report Resource Website 1+ mentions |
SNP2TFBS (RRID:SCR_016885) | SNP2TFBS | data access protocol, data or information resource, database, software resource, web service | Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs. | collection, regulatory, single, polymorphism, SNP, affecting, predicted, transcription, factor, binding, site, affinity, data, human, nucleotide, genome | Swiss Institute of Bioinformatics ; Swiss National Science Foundation |
PMID:27899579 | Free, Freely available | SCR_016885 | SciCrunch Registry | Single Nucleotide Polymorphisms 2 Transcription Factor Binding Site, SNP2TFBS | 2026-09-26 02:17:14 | 8 | |||||||
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Johns Hopkins Medicine Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core Facility Resource Report Resource Website 1+ mentions |
Johns Hopkins Medicine Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core Facility (RRID:SCR_017172) | SCTC, JHMI, JHU | access service resource, analysis service resource, core facility, production service resource, service resource | Core provides assistance with Single Cell RNA and DNA Sequencing, Spatial Transcriptomics, Next-Generation Sequencing libraries. | single, cell, spatial, omics, next, generation, sequencing, DNA, RNA | Restricted | SCR_017172 | SciCrunch Registry | , Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core | 2026-09-26 02:17:17 | 1 | |||||||||
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University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility Resource Report Resource Website |
University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility (RRID:SCR_017177) | University of Manitoba BIT Core Facility | access service resource, analysis service resource, core facility, data analysis service, data or information resource, production service resource, service resource, software resource | BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management. | bioinformatics, genome, assembly, microarray, transcriptomics, pathway, data, analysis, management | Restricted | SCR_017177 | SciCrunch Registry | University of Manitoba, BIT, Bio Information Technologies Lab, Fritensky Lab, Canada, Department of Plant Science | 2026-09-26 02:17:15 | 0 | |||||||||
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Drop-seq tools Resource Report Resource Website 100+ mentions |
Drop-seq tools (RRID:SCR_018142) | data analysis software, data processing software, software application, software resource | Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript. | Simultaneous analysis, Drop-seq data, gene expression, thousands individual cells |
is listed by: Debian has parent organization: Broad Institute |
Klarman Cell Observatory ; MGH Psychiatry Residency Research Program ; NHGRI P50 HG006193; NICHD F32 HD075541; NIMH R25 MH094612; NIMH U01 MH105960; NSF DMR 1310266; NSF DMR 1420570; NSF ECS 0335765; Simons Foundation ; Stanley Center for Psychiatric Research ; Stanley-MGH Fellowship in Psychiatric Neuroscience ; Stewart Trust Fellows Award |
PMID:26000488 | https://sources.debian.org/src/drop-seq-tools/ | SCR_018142 | SciCrunch Registry | Droplet sequencing tools, Droplet sequencing data analysis software tools | 2026-09-26 02:17:15 | 112 | |||||||
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MetaNeighbor Resource Report Resource Website 50+ mentions |
MetaNeighbor (RRID:SCR_016727) | data analysis software, data processing software, software application, software resource | Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting. | quantify, cell, type, replicability, dataset, access, cell, type, identity, functional, random, gene |
is used by: BICCN is listed by: Bioconductor is listed by: OMICtools |
Free, Available for download, Freely available | https://github.com/maggiecrow/MetaNeighbor, https://github.com/gillislab/MetaNeighbor | SCR_016727 | SciCrunch Registry | 2026-09-26 02:17:17 | 58 | |||||||||
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OMiCC Resource Report Resource Website 1+ mentions |
OMiCC (RRID:SCR_016604) | OMiCC | analysis service resource, data analysis service, data or information resource, production service resource, service resource, software resource, web application | Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | creating, metadata, analysis, annotated, gene, expression, data, compendia, human, mouse |
uses: Gene Expression Omnibus has parent organization: NIAID |
PMID:27323300 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016604 | SciCrunch Registry | OMics Compendia Commons | 2026-09-26 02:17:14 | 3 | |||||||
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STENCIL Resource Report Resource Website 1+ mentions |
STENCIL (RRID:SCR_021878) | data processing software, data visualization software, software application, software resource | Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise. | Visualizing genomic data, sharing genomic data, interactive genomic data visualizations, interpret sequencing data | NIEHS ES013768; NIGMS GM125722 |
DOI:10.1101/2021.06.04.447108 | Free, Available for download, Freely available | SCR_021878 | SciCrunch Registry | 2026-09-26 02:17:17 | 4 | |||||||||
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OpticalMapping.info Resource Report Resource Website |
OpticalMapping.info (RRID:SCR_017146) | data or information resource, portal, software resource, topical portal | Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data. | platform, tutorial, experimental, design, data, analysis, optical, mapping, structural, labelling, pattern, long, DNA, molecule, fluorescent, signal, capture | Free, Freely available | SCR_017146 | SciCrunch Registry | 2026-09-26 02:17:15 | 0 | |||||||||||
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GLIMMPSE Resource Report Resource Website 1+ mentions |
GLIMMPSE (RRID:SCR_016297) | data access protocol, software resource, web service | Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering. | power, multivariate, linear, models, Gaussian, error, Java, web, calculate | NIGMS R01 GM121081; NIGMS R25 GM111901; NLM G13 LM011879 |
PMID:24403868 PMID:40901910 |
Free, Freely available | SCR_016297 | SciCrunch Registry | , GLIMMPSE Version 3 | 2026-09-26 02:17:14 | 9 | ||||||||
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Panaroo Resource Report Resource Website 10+ mentions |
Panaroo (RRID:SCR_021090) | data analysis software, data processing software, software application, software resource | Software pipeline for pangenome investigation. Shares information between genomes to correct errors. Can call large structural variants.Fast and scalable to over 10k bacterial genomes. | pangenome investigation, correct errors, genomes, large structural variants, bacterial genomes | Free, Available for download, Freely available | https://gtonkinhill.github.io/panaroo/#/gettingstarted/quickstart | SCR_021090 | SciCrunch Registry | Bacterial Pangenome Analysis Pipeline | 2026-09-26 02:17:18 | 32 | |||||||||
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Tandem Repeats Finder Resource Report Resource Website 100+ mentions |
Tandem Repeats Finder (RRID:SCR_022065) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to locate and display tandem repeats in DNA sequences. Used to analyze DNA sequences. | locate and display tandem repeats, analyze DNA sequences, tandem repeat, DNA sequence | PMID:9862982 | Free, Available for download, Freely available | SCR_022065 | SciCrunch Registry | 2026-09-26 02:17:17 | 443 | ||||||||||
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Shannon Resource Report Resource Website 1+ mentions |
Shannon (RRID:SCR_017037) | data analysis software, data processing software, software application, software resource | Software tool for de novo transcriptome assembly from RNA-Seq data. | de novo, transcriptome, assembly, RNAseq, data |
has parent organization: University of Washington; Seattle; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Stanford University; Stanford; California |
NHGRI ; NSF Center for Science of Information ; University of Washington |
Free, Available for download, Freely available | http://sreeramkannan.github.io/Shannon/ | SCR_017037 | SciCrunch Registry | 2026-09-26 02:17:15 | 2 | ||||||||
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NiMARE Resource Report Resource Website 10+ mentions |
NiMARE (RRID:SCR_017398) | NiMARE | data analysis software, data processing software, software application, software resource | Software Python package for coordinate and image based meta analysis of neuroimaging data. | Coordinate, image, based, meta, analysis, neuroimaging, data |
uses: PyMARE is used by: Neurosynth Compose |
Free, Available for download, Freely available | https://nimare.readthedocs.io/en/latest/ | SCR_017398 | SciCrunch Registry | Neuroimaging Meta Analysis Research Environment, Neuroimaging Meta-Analysis Research Environment | 2026-09-26 02:17:15 | 17 | |||||||
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NONMEM Resource Report Resource Website 10+ mentions |
NONMEM (RRID:SCR_016986) | Nonmem | data analysis software, data processing software, simulation software, software application, software resource | Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions. | nonlinear, mixed, effect, modeling, pharmacokinetic, pharmacodynamic, analysis, data | is listed by: SoftCite | Commercially available | SCR_016986 | SciCrunch Registry | NONMEM 7.4, NONMEM 7, Nonlinear mixed effects modelling software, NONMEM 7.2, NONlinear Mixed Effects Modeling software, population analysis | 2026-09-26 02:17:15 | 45 |
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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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