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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AutoPilot Resource Report Resource Website 1+ mentions |
AutoPilot (RRID:SCR_021518) | software toolkit, software resource | Software tool as open source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Toolkit of flexible modules to design experiments without rigid programming and API limitations. | Running behavioral experiments, automating behavioral experiments, Raspberry Pis, design experiments modules, OpenBehavior |
is listed by: OpenBehavior is related to: AutoPilot project |
DOI:10.1101/807693 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/autopilot/ | SCR_021518 | Autopilot | 2026-08-02 09:08:12 | 1 | |||||||
|
jMRUI Resource Report Resource Website 1+ mentions |
jMRUI (RRID:SCR_021893) | software toolkit, software resource | Software package for advanced time domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data. | time domain analysis, magnetic resonance spectroscopy, magnetic resonance spectroscopy data analysis, spectroscopic imaging, spectroscopic imaging data analysis | PMID:11390270 DOI:10.1186/s12859-017-1459-5 |
http://www.jmrui.eu/ | SCR_021893 | 2026-08-02 09:08:19 | 5 | ||||||||||
|
EDTA Resource Report Resource Website 50+ mentions |
EDTA (RRID:SCR_022063) | software toolkit, software resource | Software package to filter out false discoveries in raw TE candidates and generate high quality non redundant TE library for whole genome TE annotations.Produces filtered non redundant TE library for annotation of structurally intact and fragmented elements. | automated whole-genome de-novo, TE annotation, TE library | NSF Plant Genome Research Program ; USDA National Institute of Food and Agriculture ; State of Iowa ; Canada First Research Excellence Fund Ontario |
PMID:31843001 | Free, Available for download, Freely available | SCR_022063 | Extensive de novo TE Annotator | 2026-08-02 09:08:22 | 57 | ||||||||
|
DeepPoseKit Resource Report Resource Website 1+ mentions |
DeepPoseKit (RRID:SCR_021405) | software toolkit, software resource | Software toolkit with high level API for 2D pose estimation of user defined keypoints using deep learning.Written in Python and built using Tensorflow and Keras.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior. | 2D pose estimation, animal pose estimation, animal behavior, DeepLabCut, Leap, OpenBehavior |
is listed by: OpenBehavior is related to: DeepPoseKit project |
DOI:10.7554/elife.47994 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/deepposekit/ | SCR_021405 | 2026-08-02 09:08:15 | 2 | ||||||||
|
Neurokit2 Resource Report Resource Website 50+ mentions |
Neurokit2 (RRID:SCR_021889) | software toolkit, software resource | Software Python package for neurophysiological signal processing. Used to analyze physiological data. | neurophysiological signal processing, analyze physiological data | PMID:33528817 | Free, Available for download, Freely available | https://github.com/neuropsychology/NeuroKit | SCR_021889 | 2026-08-02 09:08:19 | 74 | |||||||||
|
DeepSqueak Resource Report Resource Website 10+ mentions |
DeepSqueak (RRID:SCR_021524) | software toolkit, software resource | Software MATLAB package for high throughput ultrasonic vocalizations detection, classification, and analysis. | data quantification, ultrasonic vocalizations quantification, ultrasonic vocalization, OpenBehavior |
is listed by: OpenBehavior is related to: DeepSqueak project |
DOI:10.1038/s41386-018-0303-6 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/deepsqueak/ | SCR_021524 | 2026-08-02 09:08:13 | 10 | ||||||||
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Coselens Resource Report Resource Website 1+ mentions |
Coselens (RRID:SCR_022578) | software toolkit, software resource | Software R package to detect gene level differential selection between two groups of samples.Used for calculation of excess of non synonymous mutations between two groups. | detect gene level differential selection, selection between two groups of samples, calculation of excess mutation, non synonymous mutations, | Spanish Ministry of Science | DOI:10.1101/2022.01.10.475617 | Free, Available for download, Freely available | SCR_022578 | COnditional SELection on the Excess of NonSynonymous Substitutions | 2026-08-02 09:08:39 | 2 | ||||||||
|
EnrichedHeatmap Resource Report Resource Website 50+ mentions |
EnrichedHeatmap (RRID:SCR_023082) | software toolkit, software resource | Software R package for comprehensive visualization of genomic signal associations. Visualizes enrichment of genomic signals on specific target regions. Used to visualize e.g. how histone marks are enriched to specific sites. | visualization of genomic signal associations, enrichment of genomic signals, specific target regions, | German Cancer Research Center-Heidelberg Center for Personalized Oncology | PMID:29618320 | Free, Available for download, Freely available | https://bioconductor.org/packages/EnrichedHeatmap/ | SCR_023082 | 2026-08-02 09:08:35 | 69 | ||||||||
|
SYGNAL Resource Report Resource Website 1+ mentions |
SYGNAL (RRID:SCR_023080) | software toolkit, software resource | Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts. | Integrating genomic and transcriptomic measurements, human cohorts, transcriptional regulatory networks, integrate correlative, causal and mechanistic inference, unified framework, infers causal flow of information, mutations to TFs, miRNAs to perturbed gene expression patterns across patients, | NIGMS P50GM076547; NIGMS R01GM077398; NSF ABI NSF-1262637; NSF DBI-0640950; NCI U24CA143835; American Cancer Society Research Scholar Grant |
PMID:27426982 | Free, Available for download, Freely available | SCR_023080 | SYstems Genetic Network AnaLysis | 2026-08-02 09:08:50 | 1 | ||||||||
|
Algorithms and Framework for Nonnegative Matrix Factorization Resource Report Resource Website 1+ mentions |
Algorithms and Framework for Nonnegative Matrix Factorization (RRID:SCR_023124) | NMF | software toolkit, software resource | Software R package for nonnegative matrix factorization. Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms. | Non-negative Matrix Factorization, nonnegative matrix factorization, |
is listed by: CRAN is related to: NMF Toolbox |
South-African National Bioinformatics Network ; Science Foundation Ireland |
DOI:10.1186/1471-2105-11-367 | Free, Available for download, Freely available | SCR_023124 | Non-negative Matrix Factorization | 2026-08-02 09:08:39 | 8 | ||||||
|
Automated Fiber Quantification in Python Resource Report Resource Website 10+ mentions |
Automated Fiber Quantification in Python (RRID:SCR_023366) | pyAFQ | software toolkit, software resource | Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry. | Automates tractometry, automated delineation of major fiber tracts, individual human brains, quantification of tissue properties, tissue properties within fiber tracts, diffusion MRI data, | NIMH 1RF1MH121868; The BRAIN Initiative ; Gordon and Betty Moore Foundation ; Alfred P. Sloan Foundation ; NIBIB R01EB027585; NSF 1551330 |
PMID:35079748 | Free, Available for download, Freely available | SCR_023366 | 2026-08-02 09:08:45 | 12 | ||||||||
|
mBrainAligner Resource Report Resource Website 1+ mentions |
mBrainAligner (RRID:SCR_022791) | software toolkit, software resource | Software package provides cross modality image registration pipeline to support whole brain mapping projects. Contains three modules: (1) image preprocessing and global registration, (2) Coherent Landmark Mapping (CLM) based automatic registration, and (3) optional semi-automatic refinement. | cross modality image registration, whole brain mapping, image registration |
is provided by: BICCN is organization facet of: BICCN |
Southeast University ; NSFC ; University Synergy Innovation Program of Anhui Province ; NSFC-Guangdong Joint Fund ; Fundamental Research Funds |
PMID:34887551 | Free, Available for download, Freely available | SCR_022791 | 2026-08-02 09:08:44 | 3 | ||||||||
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Regression Modeling Strategies Resource Report Resource Website 10+ mentions |
Regression Modeling Strategies (RRID:SCR_023242) | rms | software toolkit, software resource | Software R package as collection of functions that assist with streamline modeling. Works with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression. | streamline modeling, regression models, regression, generalized linear models | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/harrelfe/rms, https://cran.r-project.org/web/packages/rms/rms.pdf | SCR_023242 | 2026-08-02 09:08:42 | 17 | ||||||||
|
MaAsLin2 Resource Report Resource Website 100+ mentions |
MaAsLin2 (RRID:SCR_023241) | software toolkit, software resource | SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. | Microbiome Multivariable Associations with Linear Models, | NSF DEB-2028280; NIAID U19AI110820; NHGRI R01HG005220; NIDDK R24DK110499; NIDDK U54DK102557 |
DOI:10.1371/journal.pcbi.1009442 | Free, Available for download, Freely available | https://huttenhower.sph.harvard.edu/maaslin/ | SCR_023241 | 2026-08-02 09:08:54 | 170 | ||||||||
|
scDblFinder Resource Report Resource Website 100+ mentions |
scDblFinder (RRID:SCR_022700) | software toolkit, software resource | Software package for detection and handling of doublets/multiplets in single cell sequencing data. | single cell sequencing data, doublets detection, multiplets detection, single cell, sequencing data | PMID:35814628 | Free, Available for download, Freely available | https://bioconductor.org/packages/scDblFinder/ | SCR_022700 | 2026-08-02 09:08:28 | 115 | |||||||||
|
FFTrees Resource Report Resource Website |
FFTrees (RRID:SCR_023359) | software toolkit, software resource | Software package as decision algorithms for solving binary classification problems. Faster and more frugal because every node allows making decision. Apart from being faster and requiring less information, FFTs tend to be robust against overfitting, and are easy to interpret, use, and communicate. | decision algorithm, solving binary classification problems, binary classification, | is listed by: CRAN | DOI:10.1017/S1930297500006239 | Free, Available for download, Freely available | https://CRAN.R-project.org/package=FFTrees | SCR_023359 | Fast-and-Frugal Trees | 2026-08-02 09:08:56 | 0 | |||||||
|
EnTAP Resource Report Resource Website 10+ mentions |
EnTAP (RRID:SCR_023010) | software toolkit, software resource | Software package as eukaryotic non model annotation pipeline.Used for bringing functional annotation to non-model eukaryotic transcriptomes to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. Addresses fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates of protein-coding transcripts. | functional annotation, non model eukaryotic transcriptomes, functional gene annotation, de novo assembled transcriptomes, non-model eukaryotes, protein-coding transcripts, | has parent organization: University of Connecticut; Connecticut; USA | DOI:10.1111/1755-0998.13106 | Free, Available for download, Freely available | SCR_023010 | Eukaryotic Non-Model Transcriptome Annotation Pipeline | 2026-08-02 09:08:35 | 16 | ||||||||
|
reshape2 Resource Report Resource Website 10+ mentions |
reshape2 (RRID:SCR_022679) | software toolkit, software resource | Software R package to flexible rearrange, reshape and aggregate data. Reshape2 is reboot of reshape package. | flexible rearrange data, reshape data, aggregate data |
is listed by: CRAN is related to: reshape is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_022679 | 2026-08-02 09:08:28 | 19 | ||||||||||
|
Peptides Resource Report Resource Website 1+ mentions |
Peptides (RRID:SCR_022675) | software toolkit, software resource | Software R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences. | physicochemical properties and indices calculations, amino acid sequences, amino acid physiochemical properties calculations |
is listed by: CRAN is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | https://github.com/dosorio/Peptides/ | SCR_022675 | 2026-08-02 09:08:27 | 7 | |||||||||
|
Epiviz Resource Report Resource Website 1+ mentions |
Epiviz (RRID:SCR_022796) | software toolkit, software resource | Software package as interactive visualization tool for functional genomics data. Interactive visual analytics for functional genomics data. | Interactive visual analytics, functional genomics data, interactive visualization tool | is provided by: BICCN | NHGRI R01 HG006102; NHGRI R01 HG005220; Illumina Corporation ; Genentech |
PMID:25086505 | Free, Available for download, Freely available | https://bioconductor.org/packages/epivizr/, https://epiviz.github.io/ | SCR_022796 | 2026-08-02 09:08:31 | 1 |
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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."
