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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
pwmenrich Resource Report Resource Website 1+ mentions |
pwmenrich (RRID:SCR_024249) | software toolkit, software resource | Software toolkit of high level functions for DNA motif scanning and enrichment analysis built upon Biostrings. Used for PWM enrichment analysis of already known PWMs. Also implements high-level functions for PWM scanning and visualisation. | DNA motif scanning and enrichment analysis, Biostrings, PWM enrichment analysis, PWM scanning and visualisation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-pwmenrich/ | SCR_024249 | 2026-08-05 10:48:00 | 3 | |||||||||
|
OBITools Resource Report Resource Website 10+ mentions |
OBITools (RRID:SCR_024141) | software toolkit, software library, software resource | Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. | analysing NGS data, DNA metabarcoding, filter and edit sequences, taxonomic annotation, analysis pipelines for DNA metabarcoding applications, | is listed by: Debian | PMID:25959493 | Free, Available for download, Freely available, | OMICS_32696 | https://sources.debian.org/src/obitools/ | SCR_024141 | obitools | 2026-08-05 10:47:59 | 37 | ||||||
|
xvector Resource Report Resource Website |
xvector (RRID:SCR_024263) | software toolkit, software resource | Software R package provides memory efficient S4 classes for storing sequences externally. | provides memory efficient S4 classes, storing sequences externally, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-xvector/ | SCR_024263 | 2026-08-05 10:48:02 | 0 | |||||||||
|
BoolNet Resource Report Resource Website 1+ mentions |
BoolNet (RRID:SCR_024264) | software toolkit, software resource | Software R package provides functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks. | reconstruct, generate, simulate, synchronous, asynchronous, probabilistic, temporal, Boolean networks, | is listed by: Debian | PMID:20378558 | Free, Available for download, Freely available, | OMICS_06963 | https://sources.debian.org/src/r-cran-boolnet/ | SCR_024264 | BoolNet: Construction, Simulation and Analysis of Boolean Networks, r-cran-boolnet | 2026-08-05 10:48:00 | 2 | ||||||
|
cmprsk Resource Report Resource Website 1+ mentions |
cmprsk (RRID:SCR_024265) | software toolkit, software resource | Software R package for estimation, testing and regression modeling of subdistribution functions in competing risks. | estimation, testing, regression modeling, subdistribution functions in competing risks, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-cmprsk/ | SCR_024265 | cmprsk: Subdistribution Analysis of Competing Risks, r-cran-cmprsk | 2026-08-05 10:48:01 | 2 | ||||||||
|
Orthanc Resource Report Resource Website 1+ mentions |
Orthanc (RRID:SCR_024145) | software toolkit, software library, software resource | Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases. | DICOM server, medical imaging, | is listed by: Debian | PMID:29725964 | Free, Available for download, Freely available, | https://sources.debian.org/src/orthanc/ | SCR_024145 | orthanc | 2026-08-05 10:47:59 | 3 | |||||||
|
bio3d Resource Report Resource Website 100+ mentions |
bio3d (RRID:SCR_024266) | software toolkit, software resource | Softwar R package for comparative analysis of protein structures. Used to process, organize and explore protein structure, sequence and dynamics data. Used to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. Enables statistical and graphical power of R environment to work with biological sequence and structural data. | comparative analysis of protein structures, process protein structure, organize and explore protein structure, sequence and dynamics data, | is listed by: Debian | PMID:16940322 | Free, Available for download, Freely available, | OMICS_12577 | https://sources.debian.org/src/r-cran-bio3d/ | SCR_024266 | r-cran-bio3d, bio3d: Biological Structure Analysis | 2026-08-05 10:48:02 | 311 | ||||||
|
NORSnet Resource Report Resource Website |
NORSnet (RRID:SCR_024146) | software toolkit, software library, software resource | Software as neural network based method that focuses on identification of unstructured loops. Trained to distinguish between very long contiguous segments with non-regular secondary structure and well-folded proteins. Trained on predicted information rather than on experimental data. | neural network based method, identification of unstructured loops, distinguish between very long contiguous and well-folded proteins, segments with non-regular secondary structure, | is listed by: Debian | PMID:17658943 | Free, Available for download, Freely available, | OMICS_16034 | https://sources.debian.org/src/norsnet/ | SCR_024146 | norsnet, Norsnet | 2026-08-05 10:47:58 | 0 | ||||||
|
OpenSurgSim Resource Report Resource Website |
OpenSurgSim (RRID:SCR_024147) | software toolkit, software library, software resource | Open source software framework that includes the necessary building blocks for surgical simulations, such as native device support, haptic feedback, graphics, discrete collision detection and physics simulation. Developers can refactor the physics engine, swap models, ODE solvers, or linear system solvers. | building blocks for surgical simulations, native device support, haptic feedback, graphics, discrete collision detection and physics simulation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/opensurgsim/, https://github.com/simquest/opensurgsim | SCR_024147 | opensurgsim | 2026-08-05 10:47:59 | 0 | ||||||||
|
DoseFinding Resource Report Resource Website 1+ mentions |
DoseFinding (RRID:SCR_024268) | software toolkit, software resource | Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology. | dose finding experiments design and analysis functions, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-dosefinding/ | SCR_024268 | DoseFinding: Planning and Analyzing Dose Finding Experiments, r-cran-dosefinding | 2026-08-05 10:48:01 | 1 | ||||||||
|
OpenIGTLink Resource Report Resource Website |
OpenIGTLink (RRID:SCR_024148) | software toolkit, software library, software resource | Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback. | Open Network Interface for Image-Guided Therapy, communication interface, image guided interventions, unified real-time communications, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/openigtlink/ | SCR_024148 | , openigtlink, Open Network Interface for Image-Guided Therapy Link | 2026-08-05 10:47:59 | 0 | ||||||||
|
distory Resource Report Resource Website |
distory (RRID:SCR_024269) | software toolkit, software resource | Software R package for geodesic distance between phylogenetic trees and associated functions. | geodesic distance, phylogenetic trees, associated functions, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_33012 | https://sources.debian.org/src/r-cran-distory/ | SCR_024269 | distory: Distance Between Phylogenetic Histories, r-cran-distory | 2026-08-05 10:48:02 | 0 | |||||||
|
alakazam Resource Report Resource Website 1+ mentions |
alakazam (RRID:SCR_024261) | software toolkit, software resource | Software R package for high-throughput adaptive immune receptor repertoire sequencing analysis. In particular, immunoglobulin sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. | high throughput adaptive immune receptor repertoire sequencing analysis, sequencing analysis, | is listed by: Debian | PMID:26069265 | Free, Available for download, Freely available, | OMICS_21399 | https://sources.debian.org/src/r-cran-alakazam/ | SCR_024261 | 2026-08-05 10:48:00 | 6 | |||||||
|
ade4 Resource Report Resource Website 10+ mentions |
ade4 (RRID:SCR_024259) | software toolkit, software resource | Software R package for multivariate data analysis. Used for analysis of one-table, two-table, three-table and K-table. | multivariate data analysis, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-ade4/ | SCR_024259 | 2026-08-05 10:48:01 | 17 | |||||||||
|
psignifit Resource Report Resource Website 1+ mentions |
psignifit (RRID:SCR_024196) | software toolkit, software library, software resource | Software toolbox to fit psychometric functions and to test hypotheses about psychometric data. | fit psychometric functions, test hypotheses, psychometric data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/psignifit/ | SCR_024196 | 2026-08-05 10:48:00 | 2 | |||||||||
|
bridgedbr Resource Report Resource Website |
bridgedbr (RRID:SCR_024231) | software toolkit, software resource | Software R pacakge provides functions and load identifier mapping databases in R. Uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files. | R functions, load identifier mapping databases in R, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-bridgedbr/ | SCR_024231 | 2026-08-05 10:48:00 | 0 | |||||||||
|
CNEr Resource Report Resource Website |
CNEr (RRID:SCR_024233) | software toolkit, software resource | Software R package provides large scale identification and advanced visualization of sets of conserved noncoding elements. | identification and advanced visualization of sets, conserved noncoding elements, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_33013 | https://sources.debian.org/src/r-bioc-cner/ | SCR_024233 | 2026-08-05 10:48:01 | 0 | ||||||||
|
genomeinfodb Resource Report Resource Website 1+ mentions |
genomeinfodb (RRID:SCR_024235) | software toolkit, software resource | Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order. | data and functions, translation between different chromosome sequence naming conventions, chromosome sequence naming conventions, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-genomeinfodb/ | SCR_024235 | 2026-08-05 10:48:00 | 3 | |||||||||
|
genomicalignments Resource Report Resource Website 100+ mentions |
genomicalignments (RRID:SCR_024236) | software toolkit, software resource | Software R package provides efficient containers for storing and manipulating short genomic alignments. This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments. | containers for storing and manipulating short genomic alignments, read counting, computing coverage, junction detection, working with nucleotide content of alignments. | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-genomicalignments/ | SCR_024236 | 2026-08-05 10:48:01 | 132 | |||||||||
|
BiocGenerics Resource Report Resource Website 10+ mentions |
BiocGenerics (RRID:SCR_024226) | software toolkit, software resource | Software R package defines many S4 generic functions used in Bioconductor. | S4 generic functions used in Bioconductor, S4 generic functions, Bioconductor, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-biocgenerics/ | SCR_024226 | 2026-08-05 10:48:00 | 23 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
