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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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h2o4gpu Resource Report Resource Website 1+ mentions |
h2o4gpu (RRID:SCR_022520) | H2o4GPU | software toolkit, software resource | Interface to H2O4GPU, collection of GPU solvers for machine learning algorithms. | Machine Learning on GPU, H2O4GPU, collection of GPU solvers |
is related to: CRAN is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | https://CRAN.R-project.org/package=h2o4gpu | SCR_022520 | 2026-08-09 09:08:18 | 1 | ||||||||
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shinythemes Resource Report Resource Website 1+ mentions |
shinythemes (RRID:SCR_022757) | software toolkit, software resource | Software R package Themes for use with Shiny. | Themes for use with Shiny |
is used by: Shiny is listed by: CRAN |
Free, Available for download, Freely available | https://rstudio.github.io/shinythemes/ | SCR_022757 | 2026-08-09 09:08:04 | 1 | |||||||||
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shinyhelper Resource Report Resource Website 1+ mentions |
shinyhelper (RRID:SCR_022755) | software toolkit, software resource | Software R package to add markdown helpfiles to shiny apps, using modal dialog boxes, with no need to observe each help button separately. | add markdown helpfiles, modal dialog boxes, help button separately |
is listed by: CRAN works with: Shiny |
Free, Available for download, Freely available | SCR_022755 | 2026-08-09 09:08:27 | 1 | ||||||||||
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BIDS-Matlab Resource Report Resource Website 1+ mentions |
BIDS-Matlab (RRID:SCR_022292) | software toolkit, software resource | Software MATLAB/Octave tools to interact with datasets conforming to Brain Imaging Data Structure format. | Brain Imaging Data Structure, BIDS, Matlab, octave tools, Brain Imaging Data Structure format, dataset Brain Imaging Data Structure format | is related to: Brain Imaging Data Structure (BIDs) | Free, Available for download, Freely available | https://zenodo.org/record/5910585#.YoLwlajMK3B, https://github.com/bids-standard/bids-matlab/tree/v0.1.0 | SCR_022292 | Brain Imaging Data Structure - Matlab | 2026-08-09 09:08:21 | 1 | ||||||||
|
ggforce Resource Report Resource Website 1+ mentions |
ggforce (RRID:SCR_022575) | software toolkit, software resource | Software R package providing missing functionality to ggplot2 through extension system introduced with ggplot2 v2.0.0. | missing functionality, ggplot2, extension system |
is related to: CRAN works with: ggplot2 |
Free, Available for download, Freely available | https://github.com/thomasp85/ggforce/, https://ggforce.data-imaginist.com/ | SCR_022575 | 2026-08-09 09:08:19 | 7 | |||||||||
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IBD Detection Tool Benchmark Tool Resource Report Resource Website 1+ mentions |
IBD Detection Tool Benchmark Tool (RRID:SCR_022850) | software toolkit, software resource | Software package as open source project benchmarks IBD detection tools with multiple measurements. | project benchmarks, IBD detection, multiple measurements | Free, Available for download, Freely available | SCR_022850 | 2026-08-09 09:08:28 | 1 | |||||||||||
|
Docker based GPU enabled Jupyterlab Resource Report Resource Website 1+ mentions |
Docker based GPU enabled Jupyterlab (RRID:SCR_022695) | software application, software resource | Open source, docker based, and GPU enabled jupyterlab notebook infrastructure that runs on public compute infrastructure of Galaxy Europe for rapid prototyping and developing end-to-end AI projects. Jupyterlab notebook in GPU enabled docker container for machine learning and deep learning. | Jupyterlab, GPU enabled jupyterlab notebook infrastructure, Galaxy Europe, public compute infrastructure | is related to: Jupyter Notebook | DOI:10.1101/2022.07.08.499333 | Free, Available for download, Freely available | biotools:gpu-enabled_docker_container_with_jupyterlab_for_ai | https://bio.tools/gpu-enabled_docker_container_with_jupyterlab_for_ai | SCR_022695 | 2026-08-09 09:08:02 | 2 | |||||||
|
Residue Iteration Decomposition Resource Report Resource Website 1+ mentions |
Residue Iteration Decomposition (RRID:SCR_022174) | RIDE | software toolkit, software resource | Software Matlab based toolbox for temporal decomposition of EEG signal. Used for decomposition, reconstruction, and single trial analysis of event related potentials. | temporal decomposition of EEG signal, EEG, event related potentials, single trial analysis, event related brain potentials, ERP, ERP decomposition method, ERP reconstruction, Latency variability, residue iteration decomposition, single trial analysis | is related to: MATLAB | Hong Kong Baptist University ; Hong Kong Research Grant Council ; National Natural Science Foundation of China ; Germany Hong Kong Joint Research Scheme |
PMID:25455337 | Free, Available for download, Freely available | SCR_022174 | Residue Iteration DEcomposition | 2026-08-09 09:08:11 | 8 | ||||||
|
Pi-based Remote Acquisition Technology for Motion Capture Resource Report Resource Website 1+ mentions |
Pi-based Remote Acquisition Technology for Motion Capture (RRID:SCR_022327) | PiRATeMC | software toolkit, software resource | Software data management pipeline for camera synchronization and combined data directories. | OpenBehavior, camera synchronization, combined data directories, data management |
is listed by: OpenBehavior is related to: Pi-based Remote Acquisition Technology for Motion Capture project |
DOI:10.1101/2021.07.23.453577 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/piratemc/ | SCR_022327 | 2026-08-09 09:07:52 | 1 | |||||||
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Joint Acquisition, Recording and Voxel based Inference System Resource Report Resource Website 1+ mentions |
Joint Acquisition, Recording and Voxel based Inference System (RRID:SCR_022723) | JARVIS | software toolkit, software resource | Software markerless 3D motion capture toolbox. Used for capturing precise 3D motion. | markerless 3D motion capture, capturing precise 3D motion | Free, Available for download, Freely available | https://github.com/JARVIS-MoCap | SCR_022723 | JARVIS-MoCap | 2026-08-09 09:08:26 | 1 | ||||||||
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zmax_edf_merge_converter Resource Report Resource Website |
zmax_edf_merge_converter (RRID:SCR_022567) | software application, software resource | Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format. | hypnodyne, Zmax, converter, EDF, merge, python, windows | Free, Available for download, Freely available | SCR_022567 | 2026-08-09 09:07:58 | 0 | |||||||||||
|
ordinal Resource Report Resource Website 1+ mentions |
ordinal (RRID:SCR_022856) | software toolkit, software resource | Software R package implementation of cumulative link models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit models. | ordered categorical data, cumulative link models, ordered regression models, proportional odds models, proportional hazards models, grouped survival times | is listed by: CRAN | Free, Available for download, Freely available | SCR_022856 | Regression Models for Ordinal Data | 2026-08-09 09:08:25 | 9 | |||||||||
|
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 | 2026-08-09 09:08:19 | 3 | ||||||||
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bio_contrast_subgraph Resource Report Resource Website 1+ mentions |
bio_contrast_subgraph (RRID:SCR_022853) | software toolkit, software resource | Software package for implementing algorithms proposed in Lanciano et al. "Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data". | , Comparing Homogeneous and Heterogeneous Networks, Omics Data | Free, Available for download, Freely available | SCR_022853 | 2026-08-09 09:08:28 | 1 | |||||||||||
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ISGPRE Resource Report Resource Website 1+ mentions |
ISGPRE (RRID:SCR_022730) | software toolkit, software resource | Software package for predicting interferon stimulated human genes. | predicting interferon stimulated human genes, interferon stimulated human genes, human genes | DOI:10.1101/2021.10.08.463622 | Free, Available for download, Freely available | http://isgpre.cvr.gla.ac.uk/ | SCR_022730 | 2026-08-09 09:08:03 | 1 | |||||||||
|
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 | 2026-08-09 09:08:12 | 78 | ||||||||
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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 | 2026-08-09 09:08:30 | 1 | ||||||||
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Algorithms and Framework for Nonnegative Matrix Factorization Resource Report Resource Website 10+ 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 | 2026-08-09 09:08:13 | 13 | ||||||
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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 | 2026-08-09 09:08:36 | 12 | ||||||||
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SigProfilerMatrixGenerator Resource Report Resource Website 10+ mentions |
SigProfilerMatrixGenerator (RRID:SCR_023122) | software application, software resource | Software tool to create mutational matrices for all types of somatic mutations. Used to generate mutational matrices for set of samples with associated mutational catalogues. Used for optimized exploration and visualization of mutational patterns for all types of small mutational events. In addition to extending classification of single base substitutions, provides support for classifying doublet base substitutions and small insertions and deletions. | mutational patterns, small mutational events, create mutational matrices, somatic mutations, samples with associated mutational catalogues, | is related to: SigProfilerExtractor | Cancer Research UK Grand Challenge Award ; Singapore Ministry of Health ; Singapore National Medical Research Council |
PMID:31470794 | Free, Available for download, Freely available | https://osf.io/s93d5/wiki/home | SCR_023122 | 2026-08-09 09:08:31 | 35 |
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