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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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R package: lattice Resource Report Resource Website 10+ mentions |
R package: lattice (RRID:SCR_015662) | data processing software, data visualization software, software application, software resource | Data visualization software inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs as well as most nonstandard requirements. | r, r package, multivariate data, data visualization | is listed by: CRAN | Free, Available for download | SCR_015662 | SciCrunch Registry | lattice, lattice: Trellis Graphics for R, Package ‘lattice’ | 2026-10-24 12:47:27 | 13 | |||||||||
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GeneMarker Resource Report Resource Website 1000+ mentions |
GeneMarker (RRID:SCR_015661) | data analysis software, data processing software, software application, software resource | Genotype analysis software which enhances the speed, accuracy, and ease of analysis. The software is an alternative to Applied BioSystems Genotyper®, GeneScan®, and other genotype analysis software. | genotype, gene analysis | is listed by: SoftCite | Commercially available, Trial available, Runs on Mac OS, Runs on Windows, Runs on Linux | SCR_015661 | SciCrunch Registry | GeneMarker: The Biologist Friendly Software | 2026-10-24 12:47:28 | 1577 | |||||||||
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LabeledIn Resource Report Resource Website 1+ mentions |
LabeledIn (RRID:SCR_015667) | data or information resource, database, software resource | Database of annotations of drug indications in FDA drug labels. LabeledIn contains an expert curated set of indications and a crowdsourced set of indications. | drug, annotation, fda, fda drug label | Intramural Research Program of the NIH – National Library of Medicine ; National Key Technology R&D Program of China 2013BAI06B01; Fundamental Research Funds for the Central Universities 13R0101; MITRE Internal Research and Development Program |
PMID:25220766 PMID:25797061 |
Public, Freely available, Free, Available for download | SCR_015667 | SciCrunch Registry | 2026-10-24 12:47:27 | 2 | |||||||||
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DISEASES Resource Report Resource Website 500+ mentions |
DISEASES (RRID:SCR_015664) | data or information resource, database | Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence. | disease, gene, disease-gene association, text-mining, , bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation Center for Protein Research NNF14CC0001; European Union Seventh Framework Programme n259348 |
PMID:25484339 | biotools:diseases | https://bio.tools/diseases | SCR_015664 | SciCrunch Registry | 2026-10-24 12:47:27 | 655 | |||||||
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TISSUES Resource Report Resource Website 10+ mentions |
TISSUES (RRID:SCR_015665) | data or information resource, database, software resource, web application | Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. | tissue expression, proteomic, transcriptomic, text-mining, brenda tissue ontology, protein identifier, bio.tools |
uses: BRENDA Tissue and Enzyme Source Ontology is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation NNF14CC0001; NCI U54 CA189205-01; CSIRO’s OCE Science Leader program |
PMID:26157623 | Freely available, Free, Available for download | biotools:tissues | https://bio.tools/tissues | SCR_015665 | SciCrunch Registry | TISSUES: Tissue Expression Database, Tissue Expression Database | 2026-10-24 12:47:28 | 45 | |||||
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MIDAS Resource Report Resource Website 1+ mentions |
MIDAS (RRID:SCR_015704) | data processing software, image analysis software, image processing software, software application, software resource | Software for processing, display, and analysis of magnetic resonance spectroscopic imaging data. MIDAS supports a "whole-brain" MRSI acquisition method that has been implemented on MRI systems from three major manufacturers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mrsi, magnetic resonance spectroscopic imaging, processing software, brain imaging | NIBIB R01EB00822; NIBIB R01EB016064 |
PMID:16763967 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015704 | SciCrunch Registry | MIDAS Software, Metabolite Imaging and Data Analysis System, MIDAS: Metabolite Imaging and Data Analysis System | 2026-10-24 12:47:28 | 1 | ||||||||
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Evolutionary Rate Covariation Resource Report Resource Website 1+ mentions |
Evolutionary Rate Covariation (RRID:SCR_015669) | ERC | data analysis software, data processing software, software application, software resource, web application | Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes. | statistical software, correlation, phylogeny, gene extraction, genetic evolutionary history, covariation, group analysis | PMID:25679399 PMID:24453993 PMID:22287101 |
Freely available, Free, Available for download | SCR_015669 | SciCrunch Registry | ERC: Evolutionary Rate Covariation, Evolutionary Rate Covariation (ERC) Analysis, Evolutionary Rate Covariation (ERC) | 2026-10-24 12:47:27 | 2 | ||||||||
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Connectivity Map 02 Resource Report Resource Website 100+ mentions |
Connectivity Map 02 (RRID:SCR_015674) | cmap | data or information resource, database, software resource, web application | Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription, expression, gene, drug, disease pattern-matching algorithm, FASEB list |
has parent organization: Broad Institute has parent organization: Broad Institute of MIT and Harvard |
PMID:17008526 | THIS RESOURCE IS NO LONGER IN SERVICE | https://www.broadinstitute.org/cmap_build01 | SCR_015674 | SciCrunch Registry | Broad Institute Connectivity Map 02 Build, cmap | 2026-10-24 12:47:27 | 243 | ||||||
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Mendeley Data Resource Report Resource Website 100+ mentions |
Mendeley Data (RRID:SCR_015671) | data or information resource, data repository, service resource, storage service resource | Cloud-based data repository for storing, publishing and accessing scientific data. Mendeley Data creates a permanent location and issues Force 11 compliant citations for uploaded data. | data repository, published data, citation, force 11, doi, dans, dans (data archiving and networking services) |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: Mendeley works with: DANS |
Free, Public, The research community can contribute to this resource, Account required | DOI:10.25504/FAIRsharing.3epmpp, DOI:10.17616/R3DD11, r3d100011868, DOI:10.17632 | https://doi.org/10.17616/R3DD11, https://doi.org/10.17616/r3dd11, https://doi.org/10.17632/, https://dx.doi.org/10.17632/, https://fairsharing.org/10.25504/FAIRsharing.3epmpp, https://doi.org/10.17616/R3DD11 | SCR_015671 | SciCrunch Registry | 2026-10-24 12:47:27 | 239 | ||||||||
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SpineML_2_BRAHMS Resource Report Resource Website 1+ mentions |
SpineML_2_BRAHMS (RRID:SCR_015640) | simulation software, software application, software resource, source code | Simulation software which can execute neural network models specified in the SpineML format (an extension of the INCF's NineML). It is used as the canonical simulator backend by SpineCreator and translates the SpineML specification of the model into object code and a SystemML specification of the network. | spineml, brahms, spinecreator, neural network, modeling software |
uses: SpineML uses: BRAHMS |
BIMPA EP/G015627/1 | PMID:24253973 | Free, Available for download | SCR_015640 | SciCrunch Registry | 2026-10-24 12:47:28 | 2 | ||||||||
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BRAHMS Resource Report Resource Website 10+ mentions |
BRAHMS (RRID:SCR_015642) | software resource | Simulation software that runs network simulations where the network is specified in its own format called SystemML. The components of the network can be implemented in C, C++, Python or Matlab and are used in SpineML_2_BRAHMS to provide a simulation back-end for SpineML models. | neural network, simulation, modeling software, spineml, systemml, c, c++, python, matlab | is used by: SpineML_2_BRAHMS | DOI:10.1016/j.aei.2009.08.002 | Free, Available for download | http://brahms.sourceforge.net/home/ | SCR_015642 | SciCrunch Registry | 2026-10-24 12:47:26 | 19 | ||||||||
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Phobius Resource Report Resource Website 500+ mentions |
Phobius (RRID:SCR_015643) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web application for combined transmembrane topology and signal peptide prediction. Used for whole genome annotation of signal peptides and transmembrane regions. Predictor is based on hidden Markov model (HMM) that models different sequence regions of signal peptide and different regions of transmembrane protein in series of interconnected states. | Signal peptide prediction, whole genome annotation, transmembrane region, protein prediction, transmembrane topology, signal peptide, fasta, hidden markov model | is listed by: SoftCite | PMID:15111065 PMID:30976793 |
Freely Available, Free, Available for download | SCR_018767 | http://phobius.binf.ku.dk/, https://www.ebi.ac.uk/Tools/pfa/phobius/ | SCR_015643 | SciCrunch Registry | PHOBIUS | 2026-10-24 12:47:26 | 553 | ||||||
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Elastica2D Resource Report Resource Website 1+ mentions |
Elastica2D (RRID:SCR_015858) | data or information resource, data processing software, data visualization software, model, software application, software resource | Software for a 2D elastic beam model that can be used to model quasistatic bending of the vibrissa to compute forces and bending moments at the base. Elastica2D is part of the Digital Rat software project that that aims to enable morphologically and mechanically accurate modelling of the rat head and vibrissal (whisker) array. | matlab, quasistatic bending, vibrissa, 2d model, elastic, elastic beam, mechanical model | is used by: MATLAB | National Science Foundation 0446391; National Science Foundation 0818414; National Science Foundation 0846088 |
PMID:22298834 | Free, Available for download | SCR_015858 | SciCrunch Registry | 2026-10-24 12:47:29 | 1 | ||||||||
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Quantum Biology Institute Resource Report Resource Website |
Quantum Biology Institute (RRID:SCR_015855) | access service resource, service resource | Institute that provides resources and researches the concepts and mechanisms which underlie the complexities of biology. In particular, it incorporates concepts in physics and mathematics to resolve, unravel, and explain complex biological mechanisms and conditions. | physics, mathematics, quantum biology, biological mechanism | Available to the scientific community | http://www.nitrc.org/projects/foliations_2050/ | SCR_015855 | SciCrunch Registry | 2026-10-24 12:47:31 | 0 | ||||||||||
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Stanford Diabetes Research Center Resource Report Resource Website 1+ mentions |
Stanford Diabetes Research Center (RRID:SCR_015856) | access service resource, service resource | University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Stanford University. | stanford, diabetes, research center, niddk, service resource |
is listed by: NIDDK Information Network (dkNET) is listed by: Diabetes Research Centers has organization facet: Stanford Diabetes Research Center Diabetes Immune Monitoring Core has organization facet: Stanford Diabetes Research Center Stanford Islet Research Core has organization facet: Stanford Diabetes Research Center Diabetes Clinical and Translational Core has organization facet: Stanford Diabetes Research Center Diabetes Genomics Analysis Core is organization facet of: Diabetes Research Centers |
NIDDK P30 DK116074 | Available to the scientific community | SCR_015856 | SciCrunch Registry | 2026-10-24 12:47:29 | 1 | |||||||||
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Clinical Trials in Organ Transplantation (CTOT) Resource Report Resource Website 1+ mentions |
Clinical Trials in Organ Transplantation (CTOT) (RRID:SCR_015859) | CTOT | consortium, data or information resource, organization portal, portal, project portal | Project portal for a cooperative research program to improve short and long-term graft and patient survival. CTOT is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for transplant recipients. | graft, graft patient, patient survival, clinical study, transplant, transplant recipient, mechanistic study |
is listed by: NIDDK Information Network (dkNET) is listed by: Diabetes Research Centers is related to: Clinical Trials in Organ Transplantation in Children (CTOT-C) |
NIAID UM2 AI117870 | Public, Available to the scientific community | SCR_015859 | SciCrunch Registry | Clinical Trials in Organ Transplantation | 2026-10-24 12:47:29 | 1 | |||||||
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Clinical Trials in Organ Transplantation in Children (CTOT-C) Resource Report Resource Website 1+ mentions |
Clinical Trials in Organ Transplantation in Children (CTOT-C) (RRID:SCR_015860) | CTOT-C | consortium, data or information resource, organization portal, portal, project portal | Project portal for a cooperative research program sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). CTOT-C is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for pediatric heart, lung, or kidney transplant recipients. | heart, kidney, lung, pediatric, cooperative research program, niaid, clinical study, mechanistic study, transplant |
is listed by: NIDDK Information Network (dkNET) is related to: Clinical Trials in Organ Transplantation (CTOT) |
NIAID UM2 AI117870 | Public, Available to the scientific community | SCR_015860 | SciCrunch Registry | NIAID Clinical Trials in Organ Transplantation in Children, Clinical Trials in Organ Transplantation in Children, NIAID CTOT-C | 2026-10-24 12:47:31 | 1 | |||||||
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Hybrid-denovo Resource Report Resource Website 1+ mentions |
Hybrid-denovo (RRID:SCR_015866) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for a de novo OTU-picking pipeline integrating single- and paired-end 16S sequence tags. It is designed to take Illumina paired-end sequencing reads as input and output the OTU BIOM table, together with their representative sequences and a phylogenetic tree of OTUs. | hybrid-denovo, 16S rRNA, microbiota pipeline, single-end, paired-end, illumina read, de novo, otu-picking pipeline, phylogenetic tree, python, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:hybrid-denovo | https://bio.tools/hybrid-denovo | SCR_015866 | SciCrunch Registry | 2026-10-24 12:47:31 | 3 | |||||||||
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RNAcompete Resource Report Resource Website 1+ mentions |
RNAcompete (RRID:SCR_015900) | data analysis software, data processing software, software application, software resource | Method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. RNAcompete identifies expected and previously unknown RNA binding preferences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rna, protein, interaction, binding, preference, rna-seq, recognition, rbp, k-mer, structured rna, unstructured rna, matlab |
uses: MATLAB has parent organization: University of Toronto; Ontario; Canada |
Canadian Foundation of Innovation ; CIHR MOP-14609; CIHR MOP-49451; CIHR MOP-93671; National Science and Engineering Research Council of Canada (NSERC) ; Natural Sciences and Engineering Research Council ; Ontario Genomics Institute ; Ontario Research Fund |
PMID:19561594 PMID:27956239 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_18668 | SCR_015900 | SciCrunch Registry | RNAcompete Tool | 2026-10-24 12:47:32 | 1 | ||||||
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UCSF ChimeraX Resource Report Resource Website 1000+ mentions |
UCSF ChimeraX (RRID:SCR_015872) | 3d visualization software, 4d visualization software, data processing software, data visualization software, software application, software resource | Software for 3D/4D image reconstruction. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. | 3d, 4d, image reconstruction, molecular visualization, biocomputing, informatics, rbvi, ucsf, chimera |
is related to: UCSF Chimera is related to: UCSF Chimera has parent organization: University of California at San Francisco; California; USA has plug in: ISOLDE |
NIGMS P41 GM103311 | SCR_015872 | SciCrunch Registry | ChimeraX | 2026-10-24 12:47:29 | 2366 |
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