Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
sandwich Resource Report Resource Website |
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 | 2026-08-04 09:46:16 | 0 | ||||||||||
|
PathoFact2 Resource Report Resource Website 1+ mentions |
PathoFact2 (RRID:SCR_027650) | software application, software resource | Software integrative pipeline for antimicrobial resistance genes, virulence factors, toxins, and biosynthetic gene clusters prediction in metagenomes. Used for predicting microbiome-based pathogenicity and resistance to better understand and address challenges posed by antimicrobial resistance and infectious diseases. | predicting microbiome-based pathogeni, antimicrobial resistance genes, virulence factors, toxin-related proteins, biosynthetic gene clusters, metagenomes | Pélican grant from the Mie and Pierre Hippert-Faber Pélican Foundation ; Luxembourg National Research Fund FNR CORE/23/BM/15886415; European Research Council ERC-CoG 863664; Luxembourg National Research Fund FNR CORE/23/BM/15886415; Luxembourg Government CoVaLux program |
DOI:10.1101/2024.12.09.627531 | Free, Available for download, Freely available | SCR_027650 | PathoFact 2.0 | 2026-08-04 09:46:15 | 2 | ||||||||
|
mplab x ide Resource Report Resource Website |
mplab x ide (RRID:SCR_027844) | software application, software resource | Software program from Microchip, serving as a comprehensive, expandable platform for developing Microchip microcontroller applications, with many integrated tools like MPLAB Code Configurator (MCC) and MPLAB XC Compilers (free versions). Incorporates tools to discover, configure, develop, debug and qualify embedded designs for most of microcontrollers and digital signal controllers. MPLAB X IDE works seamlessly with the MPLAB development ecosystem of software and tools. | developing Microchip microcontroller applications, Microchip, microcontroller applications, | Free, Available for download | SCR_027844 | , MPLAB X Integrated Development Environment (IDE), MPLAB X IDE | 2026-08-04 09:46:19 | 0 | ||||||||||
|
lda Resource Report Resource Website |
lda (RRID:SCR_027850) | software application, software resource | Software application for topic modeling with latent Dirichlet allocation. | Topic modeling, latent Dirichlet allocation, Gibbs sampling, | Free, Available for download, Freely available | SCR_027850 | 2026-08-04 09:46:18 | 0 | |||||||||||
|
Tracker Resource Report Resource Website 1+ mentions |
Tracker (RRID:SCR_027845) | software application, software resource | Software video analysis and modeling tool developed within the Open Source Physics (OSP) Java framework. Allows frame-by-frame tracking of anatomical landmarks and articulated structures from video recordings, enabling the extraction of time-dependent kinematic variables such as displacement, velocity, and acceleration. Tracker is well suited for biomechanical analyses of articulated systems, as it supports joint-based rotations, reference-frame definition, and the export of quantitative motion data for further post-processing. | frame-by-frame tracking, anatomical landmarks and articulated structures, video recordings, extraction of time-dependent kinematic variables, | Free, Available for download, Freely available | SCR_027845 | Tracker Video Analysis and Modeling | 2026-08-04 09:46:18 | 1 | ||||||||||
|
peakPick Resource Report Resource Website |
peakPick (RRID:SCR_027740) | software application, software resource | Software R package for identifying peaks in data related to genomics, genetics, or epigenetics research. | Epigenetics, SNV, indel, identifying peaks in data, genomics data, genetics data, epigenetics data, | Free, Freely available | SCR_027740 | 2026-08-04 09:46:16 | 0 | |||||||||||
|
LLM-PathwayCurator Resource Report Resource Website |
LLM-PathwayCurator (RRID:SCR_027964) | software application, software resource | Software quality-assurance layer for pathway enrichment interpretation that converts enrichment term lists into context-conditioned, evidence-linked, schema-bounded claims and assigns PASS/ABSTAIN/FAIL via predefined, rule-based audit gates (stability, context validity stress tests, evidence-link integrity, and contradiction checks), producing decision-grade reports with audit logs. The LLM is confined to proposal-only steps; final decisions are mechanical and reproducible. | quality-assurance layer, pathway enrichment interpretation, enrichment term lists, context-conditioned, evidence-linked, schema-bounded, claims, assigns PASS/ABSTAIN/FAIL audit gates, decision-grade reports with audit logs, | Free, Freely available | https://github.com/kenflab/LLM-PathwayCurator | SCR_027964 | 2026-08-04 09:46:19 | 0 | ||||||||||
|
Poly Pipeline Resource Report Resource Website |
Poly Pipeline (RRID:SCR_027993) | software application, software resource | Software data analysis pipeline for spatial transcriptomics data tailored to polyploid organisms. | Spatial transcriptomics data, polyploid organisms, data analysis, | Free, Available for download, Freely available | https://zenodo.org/records/18655692 | SCR_027993 | 2026-08-04 09:46:20 | 0 | ||||||||||
|
Spectroscopic Imaging, VIsualization, and Computing (SIVIC) Resource Report Resource Website |
Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) | SIVIC | software application, software resource | Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. | DICOM MR Spectroscopy Workflows, data processing, data visualization, DICOM MR spectroscopy data, | NCI RO1 CA127612; NCI P01 CA11816; NIBIB P41EB013598 |
PMID:23970895 | Free, Available for download, Freely available | SCR_027875 | 2026-08-04 09:46:18 | 0 | ||||||||
|
Purdue University Research Repository (PURR) Resource Report Resource Website |
Purdue University Research Repository (PURR) (RRID:SCR_027877) | PURR | storage service resource, data repository, service resource | Provides online, collaborative working space and data-sharing platform. Provides services with data management planning, boilerplate text for proposal, sample plans and individual consultation. Each dataset gets DOI. PURR publishes and archives digital datasets from researchers across campus and welcomes all kinds of open data from images and videos to spreadsheets and source code. | FAIR, DOI, open data, publishes and archives digital datasets, data-sharing platform, data management planning, boilerplate text for proposal, sample plans, consultation, | Restricted | SCR_027877 | 2026-08-04 09:46:18 | 0 | ||||||||||
|
DMRcate Resource Report Resource Website |
DMRcate (RRID:SCR_028007) | software application, software resource | Software application for de novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions. | de novo identification and extraction, differentially methylated regions, human genome, | Free, Available for download, Freely available | SCR_028007 | 2026-08-04 09:46:22 | 0 | |||||||||||
|
somalier Resource Report Resource Website |
somalier (RRID:SCR_028167) | software application, software resource | Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches. | rapid relatedness estimation, cancer and germline studies, efficient genome sketches, quality control, | NHGRI R41HG010126; NHGRI R01HG009141; NCI U24CA209999; NCI R37CA246183; NCI P30CA04014 |
PMID:32664994 | Free, Available for download, Freely available | SCR_028167 | Somalier | 2026-08-04 09:46:25 | 0 | ||||||||
|
ChatMDV Resource Report Resource Website |
ChatMDV (RRID:SCR_028342) | software application, software resource | Software tool as natural language interface integrated with MDV that allows users to generate high-quality interactive visualisations through natural language commands. ChatMDV employs a retrieval-augmented generation (RAG) pipeline combined with large language models (LLMs) to translate user queries into reproducible Python code and interactive output. Module to add chatbot functionality to query Multi-Dimensional Viewer projects. | add chatbot functionality, query Multi-Dimensional Viewer projects, | DOI:10.1101/2025.08.26.671083 | Free, Available for download, Freely available | https://github.com/Taylor-CCB-Group/MDV | SCR_028342 | 2026-08-04 09:46:24 | 0 | |||||||||
|
DAMMIF Resource Report Resource Website |
DAMMIF (RRID:SCR_028444) | software application, software resource | Software tool for rapidly determining the low-resolution three-dimensional shape of biological macromolecules in solution using Small-Angle X-ray Scattering (SAXS) data. Used for rapid ab-initio shape determination in small-angle scattering. | EMBL Hamburg BioSAXS group, determining low-resolution three-dimensional shape of biological macromolecules, macromolecules in solution, Small-Angle X-ray Scattering, | is related to: ATSAS | PMID:27630371 | Free, Available for download | SCR_028444 | Dummy Atom Model Fast | 2026-08-04 09:46:30 | 0 | ||||||||
|
GATK VariantFiltration Resource Report Resource Website |
GATK VariantFiltration (RRID:SCR_028441) | software application, software resource | Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible | hard-filtering variant callsets, annotate low-quality variants, |
is related to: GATK is organization facet of: Broad Institute |
Free, Freely available | https://gatk.broadinstitute.org/hc/en-us | SCR_028441 | 2026-08-04 09:46:30 | 0 | |||||||||
|
bedGraphToBigWig Resource Report Resource Website |
bedGraphToBigWig (RRID:SCR_028439) | software application, software resource | Command-line utility provided by the UCSC Genome Browser to convert text-based bedGraph files into indexed binary bigWig files. It is specifically used in bioinformatics to transform dense, continuous genome coverage data into a format that enables fast visualization and remote viewing in genome browsers like IGV or the UCSC Genome Browser. | Convert bedGraph file to bigWig format, convert text-based bedGraph files, indexed binary bigWig files, transform genome coverage data, |
is related to: BigWig and BigBed works with: UCSC Genome Browser |
DOI:10.1093/bioinformatics/btq351 | Free, Freely available, | SCR_028439 | 2026-08-04 09:46:25 | 0 | |||||||||
|
Simbody(tm): SimTK Multibody Dynamics Toolset Resource Report Resource Website 1+ mentions |
Simbody(tm): SimTK Multibody Dynamics Toolset (RRID:SCR_002684) | software application, simulation software, software resource | This project is a SimTK Core toolset providing general multibody dynamics capability, i.e., the capability to solve Newton's 2nd law F=ma in any set of coordinates. The techniques of rigid body mechanics are used to provide results in Order(n) time for any set of n coordinates. This can be used for internal coordinate modeling of molecules, or for coarse-grained models based on larger chunks. It is also useful for large-scale mechanical models, such as neuromuscular models of human gait. Simbody is provided as an open source, object-oriented C++ API and delivers high-performance, accuracy-controlled science/engineering-quality results. Binaries of this software are bundled with other SimTK Core modules. | articulated body, coarse-grained molecule modeling, constrained motion, internal coordinates, mechanical simulation, mechanics, molecular dynamics, multibody dynamics, rigid body, simtk core, skeletal mechanics, torsion coordinates |
is used by: CPODES numerical integrator is related to: Simtk.org |
PMID:25866705 | Free, Available for download, Freely available | nif-0000-23309 | SCR_002684 | Simbody | 2026-08-05 10:43:39 | 1 | |||||||
|
pIRS Resource Report Resource Website 50+ mentions |
pIRS (RRID:SCR_002519) | software application, simulation software, software resource | Software for de novo data simulation. It uses empirical distribution to reproduce Illumina pair-end reads with real distribution of substitution sequencing errors, quality values and GC%-depth bias. | de novo data simulation, empirical distribution, illumina pair-end read, substitution sequencing error, gc depth bias | is listed by: OMICtools | PMID:22508794 | Free, Available for download, Freely available | OMICS_00254 | SCR_002519 | pIRS (profile based Illumina pair-end Reads Simulator), profile based Illumina pair-end Reads Simulator | 2026-08-05 10:43:37 | 74 | |||||||
|
PANDA Resource Report Resource Website 100+ mentions |
PANDA (RRID:SCR_002511) | PANDA | software toolkit, software resource | Software matlab toolbox for pipeline processing of diffusion MRI images. For each subject, PANDA can provide outputs in 2 types: i) diffusion parameter data that is ready for statistical analysis; ii) brain anatomical networks constructed by using diffusion tractography. Particularly, there are 3 types of resultant diffusion parameter data: WM atlas-level, voxel-level and TBSS-level. The brain network generated by PANDA has various edge definitions, e.g. fiber number, length, or FA-weighted. The key advantages of PANDA are as follows: # fully-automatic processing from raw DICOM/NIFTI to final outputs; # Supporting both sequential and parallel computation. The parallel environment can be a single desktop with multiple-cores or a computing cluster with a SGE system; # A very friendly GUI (graphical user interface). | analyze, computational neuroscience, connectivity analysis, dicom, format conversion, gnome, linux, macos, matlab, modeling, magnetic resonance, nifti, posix/unix-like, tensor metric, tractography, workflow, xnat pipeline, diffusion mri, chinese, connectome, diffusion metrics, network, pipeline, structural connectivity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China |
National Natural Science Foundation of China ; Beijing Nova Program ; 973 program ; State Key Laboratory of Cognitive Neuroscience and Learning |
PMID:23439846 | Free, Available for download, Freely available | nlx_155911 | http://www.nitrc.org/projects/panda | SCR_002511 | PANDA: a pipeline tool for diffusion MRI, PANDA (Pipeline for Analyzing braiN Diffusion imAges), Pipeline for Analyzing braiN Diffusion imAges, PANDA: Pipeline for Analyzing braiN Diffusion imAges, panda-tool | 2026-08-05 10:43:39 | 376 | ||||
|
Brian Simulator Resource Report Resource Website 10+ mentions |
Brian Simulator (RRID:SCR_002998) | Brian | software application, simulation software, software resource | Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator. | simulation, spiking, neuron, brain, communication, modelling, computational neuroscience, python, spiking neuron, neural network |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Ecole Normale Superieure; Paris; France |
European Union ; French National Research Agency ; CNRS ; Ecole Normale Superieure; Paris; France |
DOI:10.7554/eLife.47314 DOI:10.3389/neuro.01.026.2009 DOI:10.7554/eLife.47314 |
Free, Available for download, Freely available | nif-0000-30223 | http://www.nitrc.org/projects/brian | SCR_002998 | Brian 2, Brian spiking neural network simulator, Brian2 | 2026-08-05 10:43:44 | 26 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
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.
Email: info_at_ dknet.org
