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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SwissDock Resource Report Resource Website 100+ mentions |
SwissDock (RRID:SCR_022564) | data access protocol, software resource, web service | Web service to predict molecular interactions that may occur between target protein and small molecule. Protein small molecule docking web service based on EADock DSS. | Protein small molecule docking, predict molecular interactions, target protein and small molecule interactions, | FNS 310030_130857; Swiss Institute of Bioinformatics |
PMID:21624888 | Free, Freely available | SCR_022564 | 2026-08-13 09:30:48 | 159 | |||||||||
|
SpiecEasi Resource Report Resource Website 10+ mentions |
SpiecEasi (RRID:SCR_022712) | SpiecEasi | data analysis software, data processing software, software resource, software application | Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse. | microbiome network analysis, amplicon sequencing datasets, microbial ecological networks inference | NIAID AI007180; NIDDK DK103358; NIGMS GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022712 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-08-13 09:30:51 | 20 | |||||||
|
CORAL Resource Report Resource Website 50+ mentions |
CORAL (RRID:SCR_022711) | CORAL | data analysis software, data processing software, software resource, software application | Software tool as framework for rigorous self validated data modeling and integrative, reproducible data analysis. | FAIR data, Contexton, Microtype, Data Management, Provenance, Data Analysis, Jupyter | has parent organization: University of California at Berkeley; Berkeley; USA | US Department of Energy | Free, Available for download, Freely available | SCR_022711 | Contextual Ontology based Repository Analysis Library | 2026-08-13 09:30:56 | 95 | |||||||
|
SNPRelate Resource Report Resource Website 10+ mentions |
SNPRelate (RRID:SCR_022719) | data analysis software, data processing software, software resource, software application | Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data. | parallel computing, relatedness and principal component analysis, SNP data analysis | NHGRI U01 HG 004446 | PMID:23060615 | Free, Available for download, Freely available | https://github.com/zhengxwen/SNPRelate | SCR_022719 | 2026-08-13 09:30:37 | 13 | ||||||||
|
scShapes Resource Report Resource Website 1+ mentions |
scShapes (RRID:SCR_022838) | data analysis software, data processing software, software resource, software application | Software tool as statistical framework for identifying distribution shapes in single-cell RNA-sequencing data. | Differential distributions, single-cell RNA-sequencing, zero-inflation, scRNA-seq data, modeling gene expression read counts | DOI:10.1101/2022.02.13.480299 | Free, Available for download, Freely available | SCR_022838 | 2026-08-13 09:30:39 | 1 | ||||||||||
|
University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility Resource Report Resource Website 10+ mentions |
University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility (RRID:SCR_022410) | CyTOF | core facility, service resource, storage service resource, material storage repository, access service resource | CyTOF�enables multi-parametric high-dimensional single�cell analysis�of more than 40 markers per cell, with�minimal background and compensation�issues.�Core�offers variety of�CyTOF-related services including�reagent distribution, consultation,�antibody conjugation, and data acquisition.� | USEDit, ABRF, stockroom | is listed by: ABRF CoreMarketplace | ARBF_1419 | https://coremarketplace.org?citation=1&FacilityID=1419 | SCR_022410 | University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center, IFI CyTOF Service Center | 2026-08-13 09:30:52 | 39 | |||||||
|
AxonDeepSeg Resource Report Resource Website 1+ mentions |
AxonDeepSeg (RRID:SCR_022531) | segmentation software, data processing software, software application, image analysis software, software resource | Open source software tool for automatic axon and myelin segmentation from microscopy data using convolutional neural networks. | automatically segmenting axons and myelin sheaths, microscopy images | Canada Research Chair in Quantitative Magnetic Resonance Imaging ; Canadian Institute of Health Research ; Canada Foundation for Innovation ; Natural Sciences and Engineering Research Council of Canada ; TransMedTech ; Quebec BioImaging Network |
PMID:29491478 | Free, Available for download, Freely available | SCR_022531 | 2026-08-13 09:30:35 | 1 | |||||||||
|
Bandage Resource Report Resource Website 10+ mentions |
Bandage (RRID:SCR_022772) | data analysis software, data processing software, software resource, software application | Software tool for visualising de novo assembly graphs. By displaying connections which are not present in contigs file, opens up new possibilities for analysing de novo assemblies. Used for interactive visualization of de novo genome assemblies. | interactive visualization, de novo genome assemblies, visualising de novo assembly graphs, analysing de novo assemblies |
is listed by: Debian is listed by: OMICtools |
PMID:26099265 | Free, Available for download, Freely available | OMICS_09013 | https://github.com/rrwick/Bandage, https://sources.debian.org/src/bandage/ | SCR_022772 | Bioinformatics Application for Navigating De novo Assembly Graphs Easily | 2026-08-13 09:30:53 | 27 | ||||||
|
hifiasm-meta Resource Report Resource Website 1+ mentions |
hifiasm-meta (RRID:SCR_022771) | data analysis software, data processing software, software resource, software application | Software tool as metagenome assembler that exploits high accuracy of recent data. De novo metagenome assembler, based on haplotype resolved de novo assembler for PacBio Hifi reads. Workflow consists of optional read selection, sequencing error correction, read overlapping, string graph construction and graph cleaning. | Error correction, read overlapping, hifiasm, haplotype resolved de novo assembler, PacBio Hifi reads | NHGRI R01HG010040; NHGRI U01HG010971 |
PMID:35534630 | Free, Available for download, Freely available | SCR_022771 | hifiasm_meta | 2026-08-13 09:30:57 | 2 | ||||||||
|
Cell Morphology Labelling Tool Resource Report Resource Website 1+ mentions |
Cell Morphology Labelling Tool (RRID:SCR_022770) | data or information resource, data management software, software application, image, 3d spatial image, software resource | Software tool for image quality. Used for labeling quality of images and labeling center point of 3D RI images. Used to mange 3D RI cell images taken from holotomography. | LabelingTool, holotomography, 3D RI cell image, image quality, mange 3D RI cell images | has parent organization: Yonsei University; Seoul; South Korea | Free, Available for download, Freely available | https://github.com/DigitalHealthcareLab/22CellMorphologyLabelingTool | https://github.com/DigitalHealthcareLab/22CellMorphologyLabelingTool | SCR_022770 | 22CellMorphologyLabelingTool | 2026-08-13 09:30:38 | 1 | |||||||
|
Knowledge based Identification of Pathway Enzymes Resource Report Resource Website 1+ mentions |
Knowledge based Identification of Pathway Enzymes (RRID:SCR_022370) | KIPEs | data analysis software, data processing software, software resource, software application | Software tool as automatic approach for identification of players in biosynthesis pathway. Used for automatic annotation of flavonoid biosynthesis steps in new transcriptome of genome sequence assembly. Various enzymes of entire metabolic networks can be identified if sufficient knowledge about functionally relevant amino acids is available.Combines comprehensive sequence similarity analyses with inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. | Automatic annotation, biosynthesis steps, new transcriptome of genome sequence assembly annotation, biosynthesis pathway, sequence similarity analyses, inspection of functionally relevant amino acid residues, peptide sequences | PMID:32867203 | Free, Available for download, Freely available | SCR_022370 | 2026-08-13 09:30:33 | 2 | |||||||||
|
Pediatric Cancer Data Commons Resource Report Resource Website 1+ mentions |
Pediatric Cancer Data Commons (RRID:SCR_022369) | PCDC | topical portal, data or information resource, disease-related portal, portal | PCDC brings together clinical, genomic, and imaging data from institutions around the world to transform pediatric cancer research and outcomes. Headquartered at University of Chicago, PCDC works with international leaders in pediatric cancers and National Cancer Institute to develop and apply uniform data standards that facilitate collection, combination, and analysis of data from many different sources. PCDC Consortium developes common core data dictionary and common governance structure spanning pediatric cancers neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, and Hodgkin lymphoma to enable innovative cross disease research as well as set standard for future cancer data commons endeavors. | pediatric cancer, clinical data, genomic data, imaging data, uniform data standards, common core data dictionary, common governance structure, | is related to: University of Chicago; Illinois; USA | pediatric cancer, neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, Hodgkin lymphoma | Free, Freely available | SCR_022369 | 2026-08-13 09:30:45 | 2 | ||||||||
|
Napari Resource Report Resource Website 10+ mentions |
Napari (RRID:SCR_022765) | data access protocol, software resource, web service | Multi dimensional image viewer for Python. Used for browsing, annotating, and analyzing large multi dimensional images. Can be coupled to machine learning and image analysis tools enabling more user friendly automated analysis. | Multi dimensional image viewer, large multi dimensional images, automated analysis | Free, Available for download, Freely available | https://github.com/napari/napari, https://zenodo.org/record/6598542#.YykVuHbMK3A | SCR_022765 | 2026-08-13 09:30:57 | 46 | ||||||||||
|
MUON Resource Report Resource Website 1+ mentions |
MUON (RRID:SCR_022804) | data analysis software, data processing software, software resource, software application | Software Python framework designed to work with multimodal omics data. Aims to provide convenience and speed to its users enabling standardised analysis while staying flexible and expandable. Muon stands on shoulders of and integrates with annotated data object specification and scanpy library for single cell analysis in Python. | Multimodal omics data, standardised analysis, annotated data object specification, scanpy, single cell analysis, Python | uses: scanpy | Free, Available for download, Freely available | https://github.com/scverse/muon | SCR_022804 | multimodal omics Python framework | 2026-08-13 09:30:53 | 5 | ||||||||
|
Megadepth Resource Report Resource Website 1+ mentions |
Megadepth (RRID:SCR_022779) | data analysis software, data processing software, software resource, software application | Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts. | quantifying alignments, BigWig and BAM/CRAM input files, RNA-seq reads assigned to gene in BAM file quantification, | NIGMS R01GM118568; NIGMS R01GM121459; UK Medical Research Council |
PMID:33693500 | Free, Available for download, Freely available | https://bioconductor.org/packages/megadepth | SCR_022779 | 2026-08-13 09:30:57 | 2 | ||||||||
|
University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility Resource Report Resource Website 10+ mentions |
University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility (RRID:SCR_022415) | PMBB | core facility, service resource, storage service resource, material storage repository, biobank, access service resource | BioBank supports researchers by providing centralized access to large number of annotated blood and tissue samples. | USEDit, ABRF, annotated blood and tissue samples | is listed by: ABRF CoreMarketplace | ARBF_1421 | https://coremarketplace.org?citation=1&FacilityID=1421 | SCR_022415 | University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank | 2026-08-13 09:30:34 | 16 | |||||||
|
Histological E data Registration in rodent Brain Spaces Resource Report Resource Website 1+ mentions |
Histological E data Registration in rodent Brain Spaces (RRID:SCR_022776) | HERBS | data processing software, software resource, data visualization software, software application | Open source, extendable, intuitive and interactive software platform for image visualisation and image registration. Python based GUI for histological E-data registration in brain space. | OpenBehavior, image visualisation, image registration, histological E-data registration, brain space | is listed by: OpenBehavior | DOI:10.1101/2021.10.01.462770 | SCR_022781, https://edspace.american.edu/openbehavior/project/herbs/ | SCR_022776 | 2026-08-13 09:30:38 | 1 | ||||||||
|
Adaptive Immune Receptor Repertoire Rearrangement Schema Resource Report Resource Website 1+ mentions |
Adaptive Immune Receptor Repertoire Rearrangement Schema (RRID:SCR_022592) | topical portal, data or information resource, narrative resource, standard specification, portal | Part of AIRR Data Model, defines annotations needed for rearrangements, which are sequences describing rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in tab delimited file and should be compatible with any TSV reader. Dataset is defined in this context as: TSV file, TSV with companion YAML file containing metadata, or directory containing multiple TSV files and YAML files. | AIRR Data Model, annotations needed for rearrangements, rearranged adaptive immune receptor chain sequences, | is related to: AIRR Data Commons | PMID:29144493 | Free, Freely available | https://fairsharing.org/FAIRsharing.zwjNAh | SCR_022592 | 2026-08-13 09:30:36 | 1 | ||||||||
|
OrthoVenn2 Resource Report Resource Website 100+ mentions |
OrthoVenn2 (RRID:SCR_022504) | data access protocol, software resource, web service | Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences. | whole genome comparison and annotation, orthologous clusters across multiple species, identify orthologous gene clusters, comparing multiple species protein sequences | National Natural Science Foundation of China | PMID:31053848 | Free, Freely available | SCR_022504 | 2026-08-13 09:30:48 | 288 | |||||||||
|
DIA-NN Resource Report Resource Website 100+ mentions |
DIA-NN (RRID:SCR_022865) | data analysis software, data processing software, software application, time-series analysis software, 2d time-series analysis software, software resource | Software tool for processing of data independent acquisition proteomics experiments. Universal automated software suite for DIA proteomics data analysis. Neural networks and interference correction enable deep proteome coverage in high throughput. | Neural networks, interference correction, data independent acquisition proteomics experiments, DIA proteomics data analysis | PMID:3176806 | Free, Available for download, Freely available | SCR_022865 | 2026-08-13 09:30:58 | 345 |
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.
