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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | software application, data processing software, data analysis software, software resource, software toolkit, data visualization software | Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | semantic, optimization, crystallography, chemical, editor, visualization, analysis, molecular, modeling, drug, design, biomolecule, simulation, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Engineering Research Development Center W912HZ-11-P-0019; NSF DMR-1005413 |
PMID:22889332 DOI:10.1186/1758-2946-4-17 |
Open source, Free, Free to download | OMICS_04967, biotools:avogadro | http://avogadro.openmolecules.net/ https://github.com/avogadro https://bio.tools/avogadro https://sources.debian.org/src/axe-demultiplexer/ |
SCR_015983 | 2026-02-17 10:03:14 | 1965 | ||||||
|
Brain Imaging Data Structure (BIDs) Resource Report Resource Website 100+ mentions |
Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) | BIDS | data or information resource, narrative resource, portal, standard specification | Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data. | Data storing structure, neuroimaging, standardized template, data sharing, MRI data, MEG data, EEG data, iEEG data, FASEB list |
is used by: OpenNeuro is used by: SPARC Portal is used by: SPARC Data Standard is listed by: FAIRsharing is related to: BIDS-Matlab is related to: NiPoppy works with: MNE-BIDS |
International Neuroinformatics Coordinating Facility ; Laura and John Arnold Foundation ; NIGMS P20 GM103472; Wellcome Trust ; NIAAA U01 AA021697; NIMH Intramural Research Program ; German federal state of Sachsen-Anhalt ; European Regional Development Fund ; Medical Research Council United Kingdom ; NSF 1429999 |
PMID:27326542 PMID:29917016 PMID:31239435 PMID:31239438 PMID:37744469 |
Free, Freely available | https://bids-specification.readthedocs.io/en/stable/, https://doi.org/10.25504/FAIRsharing.rd1j6t | SCR_016124 | Brain Imaging Data Structure, BIDS, Brain Imaging Data Structure (BIDS), Brain Imaging Data Structure v1.4.0 | 2026-02-17 10:02:58 | 212 | |||||
|
Linear Fascicle Evaluation Resource Report Resource Website 1+ mentions |
Linear Fascicle Evaluation (RRID:SCR_016153) | data analysis software, software application, data processing software, software resource | Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes. | connectome, encode, framework, neuroanatomy, tract, dissection, array, tensor, edge, node | requires: MATLAB | NSF IIS-1636893; NSF BCS-1734853; NCATS ULT TR001108; Indiana University Areas of Emergent Research initiative Learning: Brains ; Machines ; Children |
Free, Available for download, Demo available | SCR_016153 | 2026-02-17 10:02:58 | 1 | |||||||||
|
HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | software application, data processing software, data analysis software, sequence analysis software, software resource, software toolkit | Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning. | analysis, genetic, sequence, multiply, alignment, rate, pattern, data, evolution, platform, python, r, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NSF DBI-0096033; NSF DEB-9996118; NIH R01 AI47745; NIH U01 AI43638; University of California Universitywide AIDS Research Program IS02-SD-701; University of California ; San Diego Center for AIDS Research/NIAID Developmental Award 2 P30 AI36214; NIGMS R01 |
PMID:15509596 | Free, Available for download, Freely available | SCR_016271, biotools:HyPhy, OMICS_04235 | https://sources.debian.org/src/hyphy-pt/ https://veg.github.io/hyphy-site/ https://github.com/veg/hyphy https://bio.tools/HyPhy |
SCR_016162 | HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt | 2026-02-17 10:02:39 | 1497 | |||||
|
Mapping Population-based Structural Connectomes Resource Report Resource Website |
Mapping Population-based Structural Connectomes (RRID:SCR_016232) | data analysis software, software application, data processing software, software resource | Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis. | dwi, t1, tractography, algorithm, white matter, bundle, gray matter, shape, analysis, network, workflow | NIMH MH086633; NIMH MH092335; NSF SES-1357666; NSF DMS-1407655; CPRIT RR150054; NSF DMS1127914 |
Free for non-commercial use, Available for download | SCR_016232 | 2026-02-17 10:02:40 | 0 | ||||||||||
|
nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | software application, data processing software, data analysis software, software resource, software toolkit, data visualization software | Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data. | model, modelling, python, neuroelectrophysiology, object, neuroimaging, analysis, neurophysiology, electrophysiology, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF CBET-1351692; NSF IOS-1550994; Human Frontiers Science Program RGY0088 |
Free, Available for download, Freely available | SCR_016209 | Nelpy (Neuroelectrophysiology) | 2026-02-17 10:03:20 | 3 | ||||||||
|
Centrifuge Classifier Resource Report Resource Website 1+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
U. S. Army Research Office W911NF1410490; NSF ABI1356078; NHGRI R01 HG006677; NIGMS R01 GM083873 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge https://bio.tools/centrifuge https://sources.debian.org/src/centrifuge/ |
SCR_016665 | 2026-02-17 10:02:44 | 9 | ||||||
|
Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | software application, data processing software, data analytics software, data analysis software, software resource, sequence analysis software | Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. | gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF 1640775 | Free, Available for download, Freely available | biotools:Libra_k-mer | https://bio.tools/Libra_k-mer | SCR_016608 | 2026-02-17 10:03:28 | 0 | |||||||
|
TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | software application, data processing software, data analysis software, software resource, software toolkit | Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, topological, domain, genome, structure, linear, time, data, analysis |
has parent organization: University of Southern California; Los Angeles; USA works with: CCTOP |
NHLBI U01 HL108634; NIDDK U54 DK107981; NSF CAREER 0747475; NSF CAREER 1150287; Arnold and Mabel Beckman foundation ; Pew Charitable Trusts |
PMID:26704975 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016964 | TOPological DOMains, Topological Domains, TopDom_v0.0.2, TopDom_v0.0.1 | 2026-02-17 10:03:29 | 10 | ||||||
|
BpForms Resource Report Resource Website |
BpForms (RRID:SCR_018653) | data access protocol, web service, software toolkit, software resource | Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. | Molecular structure description, DNA, RNA, protein, modification, epigenetics, transcriptomics, post transcriptional modification, post translational modification, bio.tools |
uses: BcForms is used by: ObjTables is used by: Datanator is listed by: Debian is listed by: bio.tools is related to: BcForms is related to: ObjTables |
NIBIB P41 EB023912; NSF 1649014; NIGMS R35 GM119771 |
PMID:32423472 | Free, Freely available | biotools:bpforms | https://bio.tools/bpforms | SCR_018653 | 2026-02-17 10:03:49 | 0 | ||||||
|
ObjTables Resource Report Resource Website |
ObjTables (RRID:SCR_018652) | data management software, software application, data processing software, software resource, software toolkit | Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort. | Creating reusable dataset, combining spreadsheet with schema, spreadsheet, table, supplementary material, schema, object relational map, validation, bio.tools |
uses: BpForms uses: BcForms is listed by: bio.tools is listed by: Debian is related to: BpForms |
NIBIB P41 EB023912; NSF 1649014; NIGMS R35 GM119771 |
Free, Freely available | biotools:objtables | https://bio.tools/objtables | SCR_018652 | 2026-02-17 10:03:30 | 0 | |||||||
|
DoubletFinder Resource Report Resource Website 500+ mentions |
DoubletFinder (RRID:SCR_018771) | data analysis software, software application, data processing software, software resource | Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data. | Doublet detection in single cell RNA, single cell RNA, doublet detection, RNA sequencing data, gene expression data, artificial nearest neighbors |
is related to: Seurat has parent organization: University of California at San Francisco; California; USA |
Department of Defense Breast Cancer Research Program ; NICHD DP2 HD080351; NSF MCB 1330864; UCSF Center for Cellular Construction ; NSF Science and Technology Center ; Damon Runyon Cancer Research Foundation |
PMID:30954475 | Free, Available for download, Freely available | SCR_018771 | 2026-02-17 10:03:08 | 920 | ||||||||
|
ROSIE Resource Report Resource Website 1+ mentions |
ROSIE (RRID:SCR_018764) | ROSIE | data access protocol, application programming interface, web application, software resource | Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community. | Web interface for Rosetta, Rosetta online server, Rosetta application serverification, Rosetta user interface | works with: Rosetta | NIGMS R01 GM073151; NIGMS R01 GM07822; NIGMS R21 GM102716; NCRR R00 RR024107; NCI U54 CA143907; NEI PN2 EY016586; NIGMS T32 GM 88118; Taiwan Governmental Scholarship for Study Abroad ; Howard Hughes Medical and Institute International Student Research Fellowship ; NSF |
PMID:23717507 | Restricted | https://rosie.rosettacommons.org/ | SCR_018764 | Rosetta Online Server that Includes Everyone | 2026-02-17 10:03:48 | 7 | |||||
|
datasets.datalad.org Resource Report Resource Website 1+ mentions |
datasets.datalad.org (RRID:SCR_019089) | storage service resource, data or information resource, service resource, data set, data repository | DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data. | Version control system, data distribution, super dataset, DataLad dataset, neural data | is related to: DataLad | NSF 1429999; NSF 1912266; NIBIB P41 EB019936 |
Free, Freely available | https://www.datalad.org/datasets.html | SCR_019089 | 2026-02-17 10:03:12 | 8 | ||||||||
|
MITE-Hunter Resource Report Resource Website 1+ mentions |
MITE-Hunter (RRID:SCR_020946) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences. | Class 2 non-autonomous transposable element, genes non-coding regions, genome evolution, coding sequence, genomic DNA data sets, | NSF 0607123 | PMID:20880995 | Free, Available for download, Freely available | https://github.com/jburnette/MITE-Hunter | SCR_020946 | Miniature Inverted repeat Transposable Elements Hunter | 2026-02-17 10:03:55 | 5 | |||||||
|
BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | data analysis software, software application, data processing software, software resource | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NSF 1553680; NCRR P20 RR01 6460; NIGMS P20 GM103429 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download https://bio.tools/binpacker |
SCR_017038 | 2026-02-17 10:03:30 | 10 | ||||||
|
cytoNet Resource Report Resource Website |
cytoNet (RRID:SCR_017465) | software application, production service resource, data processing software, analysis service resource, service resource, software resource, image analysis software | Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory. | Cell, population, microscopy, image, network, analysis, quantify, structure, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1533708 | Free, Freely available | SCR_017465 | 2026-02-17 10:03:35 | 0 | |||||||||
|
Seizure-Waves Resource Report Resource Website |
Seizure-Waves (RRID:SCR_017455) | data analysis software, software application, data processing software, software resource | Analysis and modeling code for waves of seizure activity. | Analysis, modeling, wave, seizure, brain, activity, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1451384 | Free, Freely available | SCR_017455 | SeizureWaves, Seizure Waves, Seizure-Waves | 2026-02-17 10:02:52 | 0 | ||||||||
|
ChromHMM Resource Report Resource Website 10+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, software application, data processing software, software resource | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
NHGRI U54 HG004570; NHGRI RC1HG005334; NIEHS R01 ES024995; NHGRI U01 HG007912; NIMH U01 MH105578; NSF 0905968; Alfred P. Sloan Fellowship ; CAREER Award |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-02-17 10:03:01 | 47 | ||||||
|
RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | data access protocol, software application, software resource, web service, simulation software | Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model. | Protein structure predictor, 3D structure, protein sequence, secondary and tertiary structure, binding site, solvent accessibility, disordered region, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
NIGMS R01 GM089753; NSF DBI 0960390 |
PMID:21987485 | Restricted | biotools:raptorx | https://bio.tools/raptorx | SCR_018118 | 2026-02-17 10:03:01 | 149 |
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 2U24DK097771-09.
Email: info_at_ dknet.org
