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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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chip hgu133plus2 Resource Report Resource Website |
chip hgu133plus2 (RRID:SCR_027245) | software toolkit, software resource | Software R package for Affymetrix Human Genome U133 Plus 2.0 Array annotation data. | Affymetrix Human Genome U133 Plus 2.0 Array, annotation data, | Free, Available for download, Freely available, | SCR_027245 | 2026-08-09 09:09:38 | 0 | |||||||||||
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ZeroShotAMR Resource Report Resource Website 1+ mentions |
ZeroShotAMR (RRID:SCR_027224) | source code, software resource | Software repository provides the code for generalizable machine learning models for rapid antimicrobial resistance prediction in unseen healthcare settings. | generalizable machine learning models, rapid antimicrobial resistance prediction, unseen healthcare settings, | Free, Available for download, Freely available | SCR_027224 | 2026-08-09 09:09:24 | 1 | |||||||||||
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Metabolic Subphenotype Predictor Resource Report Resource Website 1+ mentions |
Metabolic Subphenotype Predictor (RRID:SCR_027192) | source code, software resource | Software repository contains code for Inference of T2D metabolic subphenotypes (MuscleIR, Beta-cell Function, Incretin Effect, Hepatic IR), Identification of dominant metabolic subphenotype, Feature extraction from glucose tiemseries, Extraction of reduced representation of glucose tiemseries,Visualization of metabolic phenotypes based on various glucose-related metrics,Concordance between CGM and Venous glucose values from at home and at clinical setting, Classification of metabolic subphenotypes. | Inference of T2D metabolic subphenotypes, identification of dominant metabolic subphenotype, extraction from glucose tiemseries, visualization of metabolic phenotypes, classification of metabolic subphenotype, s | NIDDK R01 DK110186; Stanford PHIND award ; Stanford Diabetes Research Center ; Wellcome Trust ; NIDDK U01 DK105535; NIDDK U01 DK085545; NIDDK UM1DK126185; NHLBI 2T32HL09804911 |
PMID:39715896 | Free, Available for download, Freely available | SCR_027192 | 2026-08-09 09:09:40 | 1 | |||||||||
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NanoFreeLunch Resource Report Resource Website 1+ mentions |
NanoFreeLunch (RRID:SCR_027196) | software toolkit, software resource | Software toolkit for quantitative detection of DNA methylation from nanopore sequencing data without raw signals. | quantitative detection of DNA methylation, nanopore sequencing data, data without raw signals, | Free, Available for download, Freely available | SCR_027196 | 2026-08-09 09:09:37 | 1 | |||||||||||
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IsoformSwitchAnalyzeR Resource Report Resource Website 10+ mentions |
IsoformSwitchAnalyzeR (RRID:SCR_027320) | software toolkit, software resource | Software R package to identify, annotate and visualize isoform switches with functional consequences from both short- and long-read RNA-seq data. Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc. | Identify, Annotate, Visualize, Isoform Switches with Functional Consequences, short- and long-read RNA-seq data, | Lundbeck Foundation ; Independent Research Fund Denmark |
PMID:30989184 | Free, Available for download, Freely available | SCR_027320 | 2026-08-09 09:09:25 | 12 | |||||||||
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SeSAMe Resource Report Resource Website 10+ mentions |
SeSAMe (RRID:SCR_027388) | SeSAMe | software toolkit, software resource | Software R package for reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. | reducing artifactual detection, DNA methylation, Infinium BeadChips, genomic deletions, | NCI U24 CA143882; NCI R01 CA170550; NCI U24 CA210969; Ovarian Cancer Research Fund Grant ; Michelle Lunn Hope Foundation ; Van Andel Research Institute |
PMID:30085201 | Free, Available for download, Freely available, | SCR_027388 | SEnsible Step-wise Analysis of DNA MEthylation | 2026-08-09 09:09:42 | 23 | |||||||
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MassImager Resource Report Resource Website |
MassImager (RRID:SCR_027385) | software application, software resource | Software for interactive and in-depth analysis of Mass Spectrometry Imaging (MSI) data. | Mass Spectrometry Imaging, data analysis, | PMID:29530251 | Free, Available for download, Freely available | http://www.chemmind.com/en/support_download.html | SCR_027385 | 2026-08-09 09:09:40 | 0 | |||||||||
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Dusk2Dawn Resource Report Resource Website |
Dusk2Dawn (RRID:SCR_027417) | software application, software resource | Software plugin for 'EEGLAB' MATLAB toolbox, which allows to whole-night sleep EEG using Artifact Subspace Reconstruction (ASR). Used to implement Artifact Subspace Reconstruction cleaning with whole-night sleep EEG. Automatic cleaning of whole-night sleep electroencephalogram using Artifact Subspace Reconstruction. | whole-night sleep electroencephalogram, automatic cleaning of whole-night sleep electroencephalogram, Artifact Subspace Reconstruction, implement Artifact Subspace Reconstruction cleaning, whole-night sleep EEG, | is a plug in for: EEGLAB | Free, Available for download, Freely available, | SCR_027417 | 2026-08-09 09:09:42 | 0 | ||||||||||
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SimulAdren Resource Report Resource Website |
SimulAdren (RRID:SCR_027314) | software application, software resource | Software tool as simulation program of hypothalamus-pituitary-adrenal axis (HPA axis, aka corticotropic feedback control) for education and research, based on nonlinear MiMe-NoCoDI model and implemented with CyberUnits Bricks library. | simulation program, hypothalamus-pituitary-adrenal axis, nonlinear MiMe-NoCoDI model, CyberUnits Bricks library, |
uses: CyberUnits uses: Free Pascal Compiler uses: Lazarus IDE |
DOI:10.13140/2.1.2400.2568 | Free, Available for download, Freely available | https://zenodo.org/records/16324704 | SCR_027314 | 2026-08-09 09:09:41 | 0 | ||||||||
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rfxplot Resource Report Resource Website 1+ mentions |
rfxplot (RRID:SCR_027375) | software toolkit, software resource | Software toolbox for SPM5 which offers plotting effect sizes, fitted responses, and BOLD time courses averaged across subjects from within 2nd level (random effects) analyses. The toolbox offers a large variety of plot configuration both suitable for data exploration and producing high quality figures for publications. | plot configuration, data exploration, figures for publications, plots | PMID:19140033 | Free, Available for download, Freely available | SCR_027375 | 2026-08-09 09:09:25 | 3 | ||||||||||
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HVRLocator Resource Report Resource Website 1+ mentions |
HVRLocator (RRID:SCR_027407) | software application, software resource | Software application to identify spanning hypervariable region(s) from amplicon sequencing variants or SRA public runs (SRR). Aligns query sequences to reference E. coli full-length 16S rRNA gene and identifies spanning region through alignment. Used for identifying hypervariable regions in 16S rRNA big datasets. | Align query sequences, reference E. coli full-length 16S rRNA gene, SRA public runs, 16S rRNA, Amplicon, SRA, identify spanning hypervariable region, amplicon sequencing variants, SRA public runs, identifying hypervariable regions, 16S rRNA big datasets, | German Centre for Integrative Biodiversity Research (iDiv) sIBTEDS | DOI:10.1101/2025.07.24.666487 | Free, Available for download, Freely available | https://github.com/fbcorrea/hvrlocator/ | SCR_027407 | 2026-08-09 09:09:42 | 1 | ||||||||
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openMINDS_instances Resource Report Resource Website |
openMINDS_instances (RRID:SCR_027358) | source code, software resource | Software application to provide well defined metadata instances for selected schemas of the openMINDS metadata framework. | open science, metadata instances, serviceable terminology, | is related to: openMINDS metadata framework | European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA1 720270; European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA2 785907; European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA3 945539; Helmholtz International BigBrain Analytics and Learning Laboratory (HIBALL) ; European Union’s Research and Innovation Program Horizon Europe - EBRAINS 2.0 101147319 |
Free, Available for download, Freely available, | SCR_027358 | , openMINDS instance libraries, openMINDS instances | 2026-08-09 09:09:40 | 0 | ||||||||
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Dynamont Resource Report Resource Website 1+ mentions |
Dynamont (RRID:SCR_027357) | source code, software resource | Software segmentation/resquiggling tool for ONT signals. Dynamic programming approach to segment ONT signals. | segmentation, resquiggling, ONT signals, | Free, Available for download, Freely available | , SCR_027365 | SCR_027357 | 2026-08-09 09:09:41 | 1 | ||||||||||
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bkbit Resource Report Resource Website 1+ mentions |
bkbit (RRID:SCR_027564) | software toolkit, software resource | Software package contains tools to use the BICAN Knowledgebase Data Models. | BICAN, Knowledgebase Data Models, | is organization facet of: BRAIN Initiative Cell Atlas Network | Free, Freely available | https://github.com/brain-bican/bkbit/blob/main/docs/index.rst | SCR_027564 | Brain Knowledge Base Interaction Toolkit | 2026-08-09 09:09:43 | 1 | ||||||||
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PyTorch Lightning Resource Report Resource Website 1+ mentions |
PyTorch Lightning (RRID:SCR_027468) | software application, software resource | Open-source software Python library that provides high-level interface for PyTorch deep learning framework. | Python library, interface for PyTorch, | works with: PyTorch | Restricted | SCR_027468 | 2026-08-09 09:09:41 | 3 | ||||||||||
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create_cisTarget_databases Resource Report Resource Website 10+ mentions |
create_cisTarget_databases (RRID:SCR_027473) | source code, software resource | Code to create cisTarget databases. | create cisTarget databases, cisTarget, create databases, | Free, Available for download, Freely available | SCR_027473 | 2026-08-09 09:09:26 | 14 | |||||||||||
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Nucleotide Transformer Resource Report Resource Website 1+ mentions |
Nucleotide Transformer (RRID:SCR_027472) | source code, software resource | Genomic language model trained on cross species data. | Genomic language model, trained on cross species data, cross species data, | Free, Available for download, Freely available | SCR_027472 | 2026-08-09 09:09:41 | 4 | |||||||||||
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GPS-Palm Resource Report Resource Website 1+ mentions |
GPS-Palm (RRID:SCR_027506) | software application, software resource | Software deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins. | prediction of S-palmitoylation sites, proteins, S-palmitoylation sites in proteins, S-palmitoylation sites, | Natural Science Foundation of China | PMID:32248222 | Free, Freely available, | SCR_027506 | 2026-08-09 09:09:43 | 8 | |||||||||
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sandwich Resource Report Resource Website 1+ mentions |
sandwich (RRID:SCR_027691) | software application, software resource | Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods. | covariance matrix estimators, Eicker-Huber-White sandwich covariance, sandwich covariance, | Free, Available for download, Freely available | SCR_027691 | sandwich:Robust Covariance Matrix Estimators | 2026-08-09 09:09:44 | 1 | ||||||||||
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mirt Resource Report Resource Website 1+ mentions |
mirt (RRID:SCR_027662) | mirt | software toolkit, software resource | Software package for the R Environment. Used for estimating multidimensional item response theory parameters for exploratory and confirmatory models by using maximum-likelihood meth- ods. | estimating multidimensional item response theory parameters, exploratory and confirmatory models, maximum-likelihood meth- ods, | Free, Available for download, Freely available | SCR_027662 | , mirt:Multidimensional Item Response Theory, Multidimensional Item Response Theory | 2026-08-09 09:09:29 | 2 |
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