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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRE Driver Network Resource Report Resource Website 1+ mentions |
CRE Driver Network (RRID:SCR_002720) | CRE Driver Network | biomaterial supply resource, material resource, organism supplier | Project to provide Neuroscience Community with mouse strains that are suitable for tissue and cell-type-specific perturbation of gene function in nervous system. NIH Neuroscience Blueprint has established three centers in the USA for generation of genetically modified mice expressing CRE recombinases in nervous system on the C57BJ/6 genetic background. Mouse lines are generated at Cold Spring Harbor Lab, at Scripps Research Institute, and at Baylor College of Medicine. | cre-recombinase, expression, neuroscience, mutant mouse strain, knock out mouse, phenotype, expression profile, image collection, microarray, electrophysiology, atlas, morphology, cell, annotation |
is related to: JAX Cre Repository is related to: Recombinase (cre) Activity has parent organization: NIH Blueprint for Neuroscience Research is parent organization of: Mouse Neuronal Expression Database |
NIH Blueprint for Neuroscience Research ; NIH |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-23753 | SCR_002720 | Mouse Models for Neuroscience Research, CRE-driver Network, CRE-Driver Network, NIH Neuroscience Blueprint CRE Driver Network | 2026-08-03 09:32:07 | 9 | ||||||
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Special Mouse Strains Resource Resource Report Resource Website |
Special Mouse Strains Resource (RRID:SCR_002885) | SMSR | biomaterial supply resource, material resource, organism supplier | Resource of special strains of mice that are valuable tools for genetic analysis of complex diseases. They include panels of recombinant inbred (RI) and chromosome substitution (CS) strains. | strain panel, frozen, cryopreserved, recombinant inbred mouse, chromosome substitution mouse, consomic strain, gene, disease, strain |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: Mouse Phenome Database (MPD) has parent organization: Jackson Laboratory |
Recombinant inbred mouse, Chromosome substitution mouse, Consomic strain | NCRR P40 RR016049; NIH Office of the Director P40 OD011102 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25593 | SCR_002885 | Special Mouse Strains Resource (SMSR) | 2026-08-03 09:31:52 | 0 | |||||
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Development of a Specific-Pathogen-Free Baboon Colony Resource Report Resource Website |
Development of a Specific-Pathogen-Free Baboon Colony (RRID:SCR_002900) | Development of a SPF Baboon Colony | biomaterial supply resource, material resource, organism supplier | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Program developing a self-sustaining colony of baboons free of all known herpesviruses, four retroviruses, and SV40 for research. When the program is fully developed, they will provide healthy, behaviorally normal, SPF baboons that are free of all known herpes viruses, four retroviruses, and SV40. To accomplish this goal, the center has established in collaboration with co-investigators and consultants serological and PCR tests for each of the 11 target viruses. These baboon viruses include six herpesviruses (analogs of human HSV, VZV, CMV, HHV6, EBV, and HHV8), four retroviruses (simian foamy virus, SRV/D, SIV, and STLV), and SV40. Twenty-four infant baboons are being recruited into the SPF program in each of the first five years, for a final total of at least 66 SPF baboons. All infants will be repeatedly tested for each of the target viruses. At one month of age, larger social groups of 4-6 SPF animals are formed. Beginning at 2-3 years of age, SPF animals will be integrated into larger socially compatible groups. These groups will eventually mature into breeding harems of SPF animals. This approach provides infants with age-matched companions for socialization during their early period of development, minimizes opportunities for transmission of viruses to the infants from adult animals, and allows for the simultaneous elimination of many different viruses from SPF animals. | baboon, herpes virus, human, macaque, pathogen, primate, retrovirus, virus | has parent organization: University of Oklahoma; Oklahoma; USA | NCRR R24 RR016556 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25871 | http://www.ncrr.nih.gov/comparative_medicine/resource_directory/primates.asp | SCR_002900 | 2026-08-03 09:32:10 | 0 | ||||||
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DENTIST Resource Report Resource Website 1+ mentions |
DENTIST (RRID:SCR_021856) | software toolkit, software resource | Software as automated pipeline method to close gaps in assemblies with long reads. Used to close assembly gaps using long reads at high accuracy. | genome assembly, long sequencing reads, assembly gaps | DOI:10.1101/2021.02.26.432990 | Free, Available for download, Freely available | biotools:dentist | https://bio.tools/dentist | SCR_021856 | 2026-08-02 09:08:19 | 1 | ||||||||
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imblearn Resource Report Resource Website 10+ mentions |
imblearn (RRID:SCR_021698) | software toolkit, software resource | Software Python package to tackle curse of imbalanced datasets in machine learning.Offers number of re-sampling techniques commonly used in datasets showing strong between class imbalance. | imbalanced datasets, class imbalance | Free, Available for download, Freely available | https://github.com/scikit-learn-contrib/imbalanced-learn | SCR_021698 | Imbalanced-learn | 2026-08-02 09:08:15 | 22 | |||||||||
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corticalmapping Resource Report Resource Website |
corticalmapping (RRID:SCR_021871) | software toolkit, software resource | Software package for basic visual stimulation, imaging analysis, plotting, and cell visual response properties analysis functionality for calcium imaging. | basic visual stimulation, imaging analysis, plotting, cell visual response properties analysis, functionality analysis, calcium imaging | Free, Available for download, Freely available | SCR_021871 | 2026-08-02 09:08:18 | 0 | |||||||||||
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CCP Resource Report Resource Website 1+ mentions |
CCP (RRID:SCR_021745) | software toolkit, software resource | Software R package for significance tests for canonical correlation analysis, including asymptotic tests and Monte Carlo method. | Canonical correlation, significance test | is listed by: CRAN | Free, Available for download, Freely available | SCR_021745 | Canonical Correlation Analysis | 2026-08-02 09:08:23 | 3 | |||||||||
|
Stytra Resource Report Resource Website |
Stytra (RRID:SCR_021500) | software toolkit, software resource | Open source software Python package to control stimulation and track behaviour.Provides timed stimulus presentation, interfacing with external devices and simultaneous real time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely swimming and head restrained preparations. | Control stimulation, track behaviour, closed loop behavioral experiments, larval zebrafish, behavioral parameters, position, orientation, tail, eye motion, freely swimming, head restrained, DeepLabCut, OpenBehavior |
is listed by: OpenBehavior is related to: Stytra project |
DOI:10.1371/journal.pcbi.1006699 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/stytra/ | SCR_021500 | 2026-08-02 09:08:18 | 0 | ||||||||
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Worm Behavior Platform Resource Report Resource Website |
Worm Behavior Platform (RRID:SCR_021501) | software toolkit, software resource | Software tool as repository of documentation, software, and discussions to share worm tracking data and analysis routines.Open access repository for storing, accessing, and filtering data; interchange format for notating single or multi worm behavior; and file formats written in Python for feature extraction, review, and analysis. | Worm behavior data analysis, worm behavior data sharing, worm behavior data, Caenorhabditis elegans behavioral data, Worm tracker Commons Object Notation, OpenBehavior |
is listed by: OpenBehavior is related to: Worm Behavior Platform project |
DOI:10.1038/s41592-018-0112-1 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/worm-behavior-platform/ | SCR_021501 | Tracker Commons | 2026-08-02 09:08:11 | 0 | |||||||
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Data independent acquisition proteomics workbench Resource Report Resource Website 100+ mentions |
Data independent acquisition proteomics workbench (RRID:SCR_021862) | software toolkit, software resource | Software tools for analysis of data independent acqusition type proteomics data are implemented in Galaxy framework. Enables complete DIA data analysis including spectral library generation based on DDA type data, analysis of DIA data in raw or mzml format, and differntial statistical analysis. All tools are based on open-source software such as diypasef, OpenSwath, swath2stats and MSstats. | data independent acqusition, proteomics data, Galaxy framework, | has parent organization: University of Freiburg; Baden-Wurttemberg; Germany | DOI:10.1101/2021.07.21.453197 | Free, Freely available | SCR_021862 | 2026-08-02 09:08:24 | 268 | |||||||||
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Motif Alteration Genome wide to Globally Investigate Elements Resource Report Resource Website 1+ mentions |
Motif Alteration Genome wide to Globally Investigate Elements (RRID:SCR_021903) | MAGGIE | software toolkit, software resource | Software Python package for identifying motifs mediating transcription factor binding and function. Links mutations of motif to changes of epigenomic feature without assuming linear relationship. | Identifying motifs mediating transcription factor binding, identifying motifs mediating transcription factor function, motif mutations, epigenomic feature changes | NIDDK R01 DK091183; Foundation Leducq ; Netherlands Organization for Scientific Research ; Amsterdam Cardiovascular Sciences |
PMID:32657363 | Free, Available for download, Freely available | SCR_021903 | 2026-08-02 09:08:19 | 3 | ||||||||
|
scRNAx Resource Report Resource Website |
scRNAx (RRID:SCR_022091) | software toolkit, software resource | Software pipeline to improve gene annotation for cross species analysis of single cell RNA-Seq. Cross-species transfer of high quality 3’UTR annotation for single cell RNA-Seq. | scRNA-Seq cross-species gene annotation, cross species analysis, single cell RNA-Seq | Free, Available for download, Freely available | SCR_022091 | 2026-08-02 09:08:27 | 0 | |||||||||||
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ggeffects Resource Report Resource Website 1+ mentions |
ggeffects (RRID:SCR_022496) | software toolkit, software resource | Software R package to create tidy data frames of marginal effects for ggplot from model outputs. Used to compute marginal effects and adjusted predictions from statistical models and returns result as tidy data frames. | Create tidy data frames of marginal effects, compute marginal effects, adjusted predictions, statistical models, tidy data frame |
is used by: ggplot2 is related to: CRAN |
Free, Available for download, Freely available | SCR_022496 | 2026-08-02 09:08:35 | 4 | ||||||||||
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Betareg Resource Report Resource Website 1+ mentions |
Betareg (RRID:SCR_022494) | software toolkit, software resource | Software R package for modeling beta distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of beta distributed response), bias corrected and bias reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided. | Beta regression, modeling beta distributed dependent variables, rates and proportions |
is related to: CRAN is related to: R Project for Statistical Computing |
DOI:10.18637/jss.v034.i02 | Free, Available for download, Freely available | SCR_022494 | 2026-08-02 09:08:25 | 1 | |||||||||
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BME Resource Report Resource Website 1+ mentions |
BME (RRID:SCR_021953) | software toolkit, software resource | Software Python package to construct conformational ensemble of biomolecular system by integrating molecular simulations and experimental data. Performs ensemble reweighting using Bayesian Maximum Entropy approach. | Bayesian maximum entropy, integrating molecular simulations and experimental data, ensemble reweighting, Bayesian Maximum Entropy approach | The Velux Foundations ; Novo Nordisk Foundation ; Lundbeck Foundation |
PMID:32006288 | Free, Available for download, Freely available | SCR_021953 | Bayesian/Maximum Entropy | 2026-08-02 09:08:26 | 4 | ||||||||
|
Classification And Regression Training Resource Report Resource Website 10+ mentions |
Classification And Regression Training (RRID:SCR_022524) | caret | software toolkit, software resource | Software R package that contains functions for training and plotting classification and regression models. Includes methods for pre-processing training data, calculating variable importance, and model visualizations. | training and plotting classification and regression models, pre-processing training data, calculating variable importance, model visualizations. |
is related to: CRAN is related to: R Project for Statistical Computing |
DOI:10.18637/jss.v028.i05 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/caret/ | SCR_022524 | Classification And REgression Training | 2026-08-02 09:08:31 | 35 | ||||||
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Radiant Resource Report Resource Website 1+ mentions |
Radiant (RRID:SCR_022645) | software toolkit, software resource | Software tool used to control Plexon pattern generator for optogenetic stimulation. | control Plexon pattern generator, optogenetic stimulation, Plexon Inc. | Free, Available for download, Freely available | SCR_022645 | Radiant v2.3, Radiant v2.2 | 2026-08-02 09:08:27 | 3 | ||||||||||
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simplePHENOTYPES Resource Report Resource Website 1+ mentions |
simplePHENOTYPES (RRID:SCR_022523) | software toolkit, software resource | Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy. | Multiple traits simulation, pleiotropy, partial pleiotropy, spurious pleiotropy, causal mutations affecting multiple traits |
is related to: CRAN is related to: R Project for Statistical Computing |
NSF 1733606 | PMID:33129253 | Free, Available for download, Freely available | https://github.com/samuelbfernandes/simplePHENOTYPES | SCR_022523 | Simulation of Pleiotropic, Linked and Epistatic Phenotypes | 2026-08-02 09:08:37 | 2 | ||||||
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MLSBM Resource Report Resource Website 1+ mentions |
MLSBM (RRID:SCR_021795) | software toolkit, software resource | Software R package to Fit Bayesian stochastic block models and multi level stochastic block models using efficient Gibbs sampling implemented in Rcpp. Models assume symmetric, non reflexive graphs with unweighted, binary edges. Data are input as symmetric binary adjacency matrix, or list of such matrices. | Fit Bayesian stochastic block models, multi level stochastic block models, Gibbs sampling, Rcpp | Free, Available for download, Freely available | SCR_021795 | Efficient Estimation of Bayesian SBMs and MLSBMs | 2026-08-02 09:08:17 | 2 | ||||||||||
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ranger Resource Report Resource Website 1+ mentions |
ranger (RRID:SCR_022521) | software toolkit, software resource | Software R package as fast implementation of Random Forests for high dimentional data. | Random Forest, high dimentional data |
is related to: CRAN is related to: R Project for Statistical Computing |
DOI:10.18637/jss.v077.i01 DOI:10.48550/arXiv.1508.04409 |
Free, Available for download, Freely available | https://github.com/imbs-hl/ranger | SCR_022521 | 2026-08-02 09:08:26 | 9 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
