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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ToneBox Resource Report Resource Website |
ToneBox (RRID:SCR_021548) | data or information resource, instrument resource, portal, project portal | Project related to auditory behavioral task data collection.Provided high throughput operant conditioning in mouse homecage system was developed by University of Maryland,College Park, scientists.Automated system for training up to hundreds of mice in auditory behavioral task features custom Matlab GUI running on desktop which connects to Raspberry Pi to administer auditory stimuli from USB soundcard and collects auditory data as well as licking data from water spout with commercially available capacitive sensors. Parts list and build instructions are readily available from paper and associated GitHub repository. | Instrument, auditory behavioral task, automated system, training mice, auditory behavioral task, OpenBehavior |
is listed by: OpenBehavior has parent organization: University of Maryland; Maryland; USA |
DOI:10.1523/eneuro.0121-19.2019 | Free, Freely available | SCR_021548 | 2026-09-19 12:54:54 | 0 | |||||||||
|
STARsolo Resource Report Resource Website 100+ mentions |
STARsolo (RRID:SCR_021542) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for accurate, fast and versatile mapping/quantification of single cell and single nucleus RNA-seq data. Used for mapping, demultiplexing and quantification for single cell RNA-seq. Comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR. | mapping, quantification, single cell, single nucleus, RNA-seq data, quantifying gene expression | uses: STAR | DOI:10.1101/2021.05.05.442755 | Free, Available for download, Freely available | SCR_021542 | 2026-09-19 12:54:54 | 127 | |||||||||
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CIRCexplorer2 Resource Report Resource Website 10+ mentions |
CIRCexplorer2 (RRID:SCR_021664) | data analysis software, data processing software, software application, software resource | Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs. | Decipher alternative back splicing, decifer circRNAs splicing pattern, circular RNA analysis, annotate circRNAs | Ministry of Science and Technology of China ; National Natural Science Foundation of China |
PMID:27365365 PMID:30539552 |
Free, Available for download, Freely available | SCR_021664 | 2026-09-19 12:54:56 | 49 | |||||||||
|
Ratcave Resource Report Resource Website |
Ratcave (RRID:SCR_021599) | software library, software resource, software toolkit | Software 3D graphics python package for cognitive psychology experiments. Open source, cross platform Python library that adds 3D stimulus support to all OpenGL-based 2D Python stimulus libraries. These libraries include VisionEgg, Psychopy, Pyglet, and PyGam. | Stimuli to subjects, response record, Python, 3D graphics library, 3D stimulus support, OpenBehavior |
is listed by: OpenBehavior is related to: Ratcave project |
DOI:10.3758/s13428-019-01245-x | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/ratcave/ | SCR_021599 | 2026-09-19 12:54:55 | 0 | ||||||||
|
SourceMD Resource Report Resource Website |
SourceMD (RRID:SCR_021633) | data access protocol, data or information resource, software resource, web service | Web tool as prototype service to automatically generate Wikidata items using metadata from scholarly publications. Citation lookup tool in Wikipedia platform. Takes persistent identifier for scholarly article and processes it by importing bibliographic metadata into Wikidata items. In August 2018, it was merged with ORCIDator into single tool that allows for fully automated batch processing based on ISBN-13, DOI, ORCID iD, PubMed ID, PMCID identifiers. | Generate Wikidata items, scholarly publications metadata, citation lookup tool, Wikipedia platform, importing bibliographic metadata | is related to: Wikidata | Free, Freely available | https://www.wikidata.org/wiki/Wikidata:SourceMD, https://sourcemd.toolforge.org/, | SCR_021633 | Source M.D., Source Metadata Tool | 2026-09-19 12:54:56 | 0 | ||||||||
|
MNE Scan Resource Report Resource Website 1+ mentions |
MNE Scan (RRID:SCR_021530) | data acquisition software, data processing software, software application, software resource | Software tool for real time processing of electrophysiological data. | Electrophysiological data processing, medical regulatory requirements, build standalone applications, MEG data acquisition, MEG data processing, EEG data acquisition, MEG data acquisition, OpenBehavior |
is listed by: OpenBehavior is related to: MNE Scan project |
DOI:10.1016/j.jneumeth.2018.03.020 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/mne-scan/ | SCR_021530 | 2026-09-19 12:54:54 | 1 | ||||||||
|
NetMHC Resource Report Resource Website 10+ mentions |
NetMHC (RRID:SCR_021651) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for binding prediction of peptides to MHC class I molecules. The newest version NetMHC- 4.0 is used for prediction of peptide MHC class I binding affinity using gapped sequence alignment that allows insertions and deletions in alignment. | Gapped sequence alignment, peptide-MHC, artificial neural networks, MHC class I system, histocompatibility complex, peptide binding, binding prediction | PMID:18463140 PMID:26515819 |
Free, Freely available | SCR_021651 | NetMHC- 3.0, NetMHC- 2.1, NetMHC- 2.0, NetMHC- 1.0, NetMHC- 3.2, NetMHC- 4.0, NetMHC-3.4 | 2026-09-19 12:54:56 | 39 | |||||||||
|
Cumulus Resource Report Resource Website 1+ mentions |
Cumulus (RRID:SCR_021644) | data analysis software, data processing software, software application, software resource | Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. | Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data |
uses: Pegasus uses: Cirrocumulus uses: Pegasus-fus is listed by: Terra is related to: BICCN has parent organization: Broad Institute |
Frederick National Laboratory for Cancer Research ; HHMI ; Klarman Cell Observatory ; Leidos Biomedical Research ; Ludwig Center at MIT ; Manton Foundation ; NCI |
DOI:10.1038/s41592-020-0905-x | Free, Available for download, Freely available | https://app.terra.bio/#workspaces/kco-tech/Cumulus, https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst | SCR_021644 | 2026-09-19 12:54:56 | 3 | |||||||
|
jcvi Resource Report Resource Website 10+ mentions |
jcvi (RRID:SCR_021641) | software library, software resource, software toolkit | Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. | Python libraries, parse bioinformatics files, assembly, annotation, comparative genomics | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/tanghaibao/jcvi/tree/v0.5.7, https://zenodo.org/record/31631#.YRaieYhKhPa | SCR_021641 | jcvi_PyPI, jcvi 1.1.17 | 2026-09-19 12:54:56 | 20 | ||||||||
|
PANC-DB Resource Report Resource Website 1+ mentions |
PANC-DB (RRID:SCR_021860) | data or information resource, database, portal, topical portal | Portal to make all Human Pancreas Analysis Program data available to anyone in research community and to interact with and connect scientific community. Stores clinical, molecular, cellular, immunology, imaging, and pathology data from pancreatic tissue and cell samples from organ donors with and without type 1 or type 2 diabetes. | HIRN, HPAP, Human Pancreas Analysis Program, |
is listed by: NIDDK Information Network (dkNET) is related to: Human Islet Research Network (HIRN) |
Free, Freely available | SCR_021860 | 2026-09-19 12:54:59 | 1 | ||||||||||
|
Sustainable Grazing System Pasture Model Resource Report Resource Website |
Sustainable Grazing System Pasture Model (RRID:SCR_021854) | simulation software, software application, software resource | Software tool as biophysical simulation model for livestock systems. It has flexible interface for setting up and running simulations with extensive graphical and data output. | simulation model, livestock systems | Free, Available for download, Freely available | SCR_021854 | SGS Pasture Model | 2026-09-19 12:54:59 | 0 | ||||||||||
|
Million Veteran Program Resource Report Resource Website 100+ mentions |
Million Veteran Program (RRID:SCR_021731) | MVP | data or information resource, portal, topical portal | National research program to learn how genes, lifestyle, and military exposures affect health and illness. | Genomic dataset, genes, lifestyle, military exposures, affect health, affect illness | Free, Freely available | SCR_021731 | 2026-09-19 12:54:57 | 273 | ||||||||||
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FuzzyWuzzy Resource Report Resource Website 1+ mentions |
FuzzyWuzzy (RRID:SCR_021699) | data analytics software, software application, software resource, software toolkit | Software pacakge that uses Levenshtein Distance to calculate differences between sequences for string matching. | Levenshtein Distance, calculate differences between sequences, string matching | Free, Freely available | SCR_021699 | 2026-09-19 12:54:57 | 5 | |||||||||||
|
GE: Amersham Imager 600 Resource Report Resource Website 1+ mentions |
GE: Amersham Imager 600 (RRID:SCR_021853) | instrument resource | Amersham Imager 600 is CCD camera system that produces digitial images of samples in gels or membranes in three different modes: chemiluminescence, colorimetric and fluorescent image capture. Provides imaging system to capture and analyze protein and DNA sample gels and membranes in high resolution. | USEDit, chemiluminescence, colorimetric, fluorescent, image capture, digitial images | is listed by: USEDit | Commercially available | https://photos.labwrench.com/equipmentManuals/19468-6742.pdf | SCR_021853 | GE Healthcare Amersham Imager 600, Amersham Imager 600 | 2026-09-19 12:54:59 | 9 | ||||||||
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BorutaShap Resource Report Resource Website 1+ mentions |
BorutaShap (RRID:SCR_021696) | software resource | Software tool as wrapper feature selection method which combines both Boruta feature selection algorithm with shapley values. | Wrapper feature selection method, Boruta feature selection algorithm, shapley values | Free, Available for download, Freely available | https://github.com/Ekeany/Boruta-Shap | SCR_021696 | 2026-09-19 12:54:57 | 7 | ||||||||||
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LightGBM Resource Report Resource Website 10+ mentions |
LightGBM (RRID:SCR_021697) | software resource | Software tool as gradient boosting framework that uses tree based learning algorithms. Designed to be distributed and efficient with advantages:Faster training speed and higher efficiency;Lower memory usage;Better accuracy;Support of parallel, distributed, and GPU learning;Capable of handling large scale data. | Gradient boosting framework | Free, Available for download, Freely available | https://github.com/Microsoft/LightGBM/blob/master/docs/index.rst | SCR_021697 | 2026-09-19 12:54:57 | 28 | ||||||||||
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pyxDamerauLevenshtein Resource Report Resource Website 1+ mentions |
pyxDamerauLevenshtein (RRID:SCR_021858) | software resource | Software tool implements Damerau-Levenshtein (DL) edit distance algorithm for Python in Cython for high performance. | Damerau-Levenshtein, edit distance algorithm | Free, Available for download, Freely available | SCR_021858 | 2026-09-19 12:54:59 | 1 | |||||||||||
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PaintOmics Resource Report Resource Website 10+ mentions |
PaintOmics (RRID:SCR_021859) | data access protocol, software resource, web service | Web tool for integrative visualization of multiple omic datasets onto KEGG pathways. Supports integrated visualization of multiple species of different biological kingdoms and offers user possibility to request any other organism present in KEGG database. | integrative visualization, multiple omic datasets, KEGG pathways, multiple species | GVA-FEDER ; Spanish Ministry of Science and Innovation |
DOI:10.1093/bioinformatics/btq594 PMID:29800320 |
Free, Freely available | SCR_021859 | PaintOmics 3, Paintomics | 2026-09-19 12:54:59 | 15 | ||||||||
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PI Motion Control Software Resource Report Resource Website |
PI Motion Control Software (RRID:SCR_021867) | software resource | Software to control positioning systems without their own macro facility. | Physik Instrumente, control positioning systems, without their own macro facility | Restricted | SCR_021867 | Physik Instrumente Motion Control Software, Motion Control Software | 2026-09-19 12:54:59 | 0 | ||||||||||
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Sample Size Shop Resource Report Resource Website 1+ mentions |
Sample Size Shop (RRID:SCR_021747) | data or information resource, portal, topical portal | Platform for multilevel and longitudinal data.Provide researchers such as behavioral and social scientists with tools and education related to study design including Calculating power and sample size for any univariate or multivariate test for general linear multivariate model, assuming fixed predictors;Producing confidence intervals on power estimates for designs with fixed predictors;Producing power calculations for designs with single Gaussian covariate;Supporting designs with unequal group sizes, and complicated covariance structures;Creating basic power curves. | multilevel data, longitudinal data, calculating power and sample size, producing confidence intervals on power estimates, producing power calculations, creating basic power curves | Free, Freely available | SCR_021747 | 2026-09-19 12:54:57 | 4 |
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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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