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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pathbase Resource Report Resource Website 10+ mentions |
Pathbase (RRID:SCR_006141) | Pathbase | ontology, data repository, storage service resource, web service, image repository, image collection, data or information resource, service resource, controlled vocabulary, data access protocol, software resource, database | Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development) | histopathology, photomicrograph, macroscopic, mutant, genetically manipulated, pathology, transgenic, rodent, mpath ontology, mouse pathology ontology, skinbase, genotype, skin, gene, tissue, hair, mutant mouse strain, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: University of Cambridge; Cambridge; United Kingdom is parent organization of: Mouse Pathology Ontology |
Lesion, Mutant mouse strain, Inbred mouse strain | North American Hair Research Society ; Ellison Medical Foundation ; European Union QLRI-1999-00320; European Union LSHG-CT-2006-037188; NCI CA089713; NCRR RR17436; NIH AR49288 |
PMID:20587689 PMID:15623888 PMID:14681470 |
Except where otherwise noted, Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, Images on the database remain the property of the persons generously allowing their images to be used and are acknowledged within each record. Images should not be modified, Reproduced or disseminated without the express permission of the submitter. | biotools:pathbase, nlx_151637 | https://bio.tools/pathbase | SCR_006141 | Pathbase - European mutant mouse pathology database | 2026-02-14 02:04:29 | 11 | |||
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Human Reference Protein Interactome Project Resource Report Resource Website 10+ mentions |
Human Reference Protein Interactome Project (RRID:SCR_015670) | HuRI | web application, portal, data or information resource, software resource, database, project portal | Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies. | protein interactome, protein-protein interaction, ppi, pairwise combination, proteome, human reference | NHGRI R01/U01HG001715; NHGRI P50HG004233; NHLBI U01HL098166; NHLBI U01HL108630; NCI U54CA112962; NCI R33CA132073; NIH RC4HG006066; NICHD ARRA R01HD065288; NICHD ARRA R21MH104766; NICHD ARRA R01MH105524; NIMH R01MH091350; NSF CCF-1219007; NSERC RGPIN-2014-03892 |
PMID:25416956 | Freely Available, Free, Available for download | SCR_015670 | HuRI: The Human Reference Protein Interactome Mapping Project | 2026-02-14 02:04:37 | 20 | |||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NHLBI U54 HL127624; NIEHS P30 ES006096; NIMH R01 MH107487; NCI T32 CA236764; NCATS UL1 TR001425; NIGMS U01 GM120953 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-02-14 02:03:42 | 4 | ||||||||
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MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | data access protocol, software resource, web service, service resource | Web service for querying or retrieving gene annotation data. | Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; NHGRI U01 HG006476; NCI K22 CA188163; NCATS UL1 TR001114; Scripps Translational Science Institute |
DOI:10.1186/s13059-016-0953-9 | Free, Freely available | biotools:mygene.info, BioTools:mygene.info | https://bio.tools/mygene.info https://bio.tools/mygene.info https://bio.tools/mygene.info |
SCR_018660 | 2026-02-14 02:03:39 | 20 | ||||||
|
TIMER Resource Report Resource Website 1000+ mentions |
TIMER (RRID:SCR_018737) | TIMER | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features. | Tumor, tumor infiltrating immune cell, immune cell, cell, analysis, cancer cell, cancer type, tumor immunological feature, tumor genomic feature, display | National Natural Science Foundation of China ; NCI CA180980; Dana-Farber Cancer Institute |
PMID:29092952 | Free, Freely available | SCR_018737 | Tumor IMmune Estimation Resource | 2026-02-14 02:03:43 | 2042 | |||||||
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ROSIE Resource Report Resource Website 1+ mentions |
ROSIE (RRID:SCR_018764) | ROSIE | data access protocol, software resource, application programming interface, web application | 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 | 2026-02-14 02:03:43 | 7 | |||||
|
CAIRN Resource Report Resource Website |
CAIRN (RRID:SCR_019101) | data visualization software, web service, data processing software, software application, data access protocol, software resource | Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions. | Deleted CNAs quantification, Copy Number Alterations, segment file, data visualization, published cancer datasets CNAs, amplified CNA quantification | Nine Girls Ask Foundation ; NCI CA207729; NIGMS GM132055; NCI CA107263; NCI CA177519; NCI CA102310; NIA AG033082; NCI P30 CA138313 |
PMID:31923184 | Free, Available for download, Freely available | https://github.com/jrdelaney/CAIRN | SCR_019101 | Copy Alterations Intuitive Rendering Navigator | 2026-02-14 02:03:48 | 0 | |||||||
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ImmuneDB Resource Report Resource Website 1+ mentions |
ImmuneDB (RRID:SCR_017125) | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features. | collect, store, analysis, B cell, T cell, immune, receptor, sequencing, data, process, raw, read | is used by: AIRR Data Commons | NIAID P01 AI106697; NIAID P30 AI0450080; NIDDK UC4 DK112217; NCI P30 CA016520 |
PMID:30298069 | Free, Available for download, Freely available | https://github.com/arosenfeld/immunedb | SCR_017125 | 2026-02-14 02:03:21 | 8 | |||||||
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Microfluidic device to attain high spatial and temporal control of oxygen Resource Report Resource Website |
Microfluidic device to attain high spatial and temporal control of oxygen (RRID:SCR_017131) | instrument resource | Device to control spatial and temporal variations in oxygen tensions to better replicate in vivo biology. Consists of three parallel connected tissue chambers and oxygen scavenger channel placed adjacent to these tissue chambers. Provides consistent control of spatial and temporal oxygen gradients in tissue microenvironment and can be used to investigate important oxygen dependent biological processes present in cancer, ischemic heart disease, and wound healing. | device, instrument, control, spatial, temporal, variation, oxygen, tension, tissue, microenvironment | NCATS UH3 TR00048; NCI R01 CA170879; NIDDK UC4 DK104202; NSF DGE-1143954 |
PMID:30571786 | SCR_017131 | 2026-02-14 02:03:15 | 0 | ||||||||||
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exRNA Atlas Resource Report Resource Website 10+ mentions |
exRNA Atlas (RRID:SCR_017221) | ontology, data repository, storage service resource, application programming interface, data analysis service, expression atlas, portal, analysis service resource, consortium, data or information resource, production service resource, organization portal, service resource, controlled vocabulary, atlas, data access protocol, software resource, database | Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data. | Differential, expression, RNA, sequencing, qPCR, data, visualization, extracellular, exRNA, atlas, repository, dataset |
is recommended by: National Library of Medicine has parent organization: Baylor College of Medicine; Houston; Texas has parent organization: exRNA |
gastric cancer, colon carcinoma, colorectal cancer, prostate carcinoma, pancreatic carcinoma, multiple sclerosis, glioblastoma multiforme, ulcerative colitis, Alzheimer's disease, ischemic stroke, intraparenchymal hemorrhage of brain, asthma, cardiovascular disorder, myocardial infarction, lupus, nephrotic syndrome, transplanted kidney present, liver disease, transplanted liver present, pre-eclampsia, Parkinson disease, intraventricular brain hemorrhage, subarachnoid hemorrhage | NIDA U54 DA036134; NCI R01 CA163849; NIGMS R25 GM056929; NCATS UH3 TR000906; NCI U19 CA179512; NIDDK P30 DK63720; NHLBI K23 HL127099; NHLBI R01 HL136685; NIA R01 AG059729; NCATS UH3 TR000943; NCI R35 CA209904; NCI CA217685; NHLBI R01 HL122547; American Cancer Society ResearchProfessor Award ; Frank McGraw Memorial Chair in CancerResearch |
PMID:30951672 | Restricted | SCR_017221 | 2026-02-14 02:03:10 | 24 | |||||||
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RobotReviewer Resource Report Resource Website 1+ mentions |
RobotReviewer (RRID:SCR_021064) | software resource, text-mining software, software application, web application | Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials. | Data automatic extraction, clinical trial reports, automatically extract key data, Evidence Based Medicine, text journal articles processing, randomized controlled trials |
is related to: Northeastern University; Massachusetts; USA is related to: University of Texas at Austin; Texas; USA |
NLM R01 LM012086; Medical Research Council UK ; NCI UH2 CA203711 |
PMID:29093610 DOI:10.1093/jamia/ocv044 |
Free, Available for download, Freely available | https://github.com/ijmarshall/robotreviewer https://robotreviewer.vortext.systems/ |
SCR_021064 | Automating Biomedical Evidence Synthesis | 2026-02-14 02:04:36 | 1 | ||||||
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SnapATAC Resource Report Resource Website 10+ mentions |
SnapATAC (RRID:SCR_020981) | data processing software, data analysis software, software toolkit, software application, software resource | Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset. | scATAC-seq datasets analysis, dissects cellular heterogeneity, cellular states, map trajectories | NCI K99 CA252020; UCSD School of Medicine ; NIMH U19 MH114831 |
PMID:33637727 | Free, Available for download, Freely available | https://github.com/r3fang/SnapATAC | SCR_020981 | Single Nucleus Analysis Pipeline for ATAC-seq | 2026-02-14 02:04:35 | 22 | |||||||
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Exemplar Microscopy Images of Tissues Resource Report Resource Website 1+ mentions |
Exemplar Microscopy Images of Tissues (RRID:SCR_021052) | EMIT | immuno detection protocol, experimental protocol, data repository, storage service resource, 2d spatial image, image collection, data set, data or information resource, immunofluorescence, service resource, image, image repository, narrative resource | Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets. | Reference dataset, multiplexed immunofluorescence microscopy images, tissue microarray, cyclic immunofluorescence, tissues images, tumors images |
is related to: Synapse is related to: Harvard Medical School; Massachusetts; USA |
glioblastoma, lung adenocarcinoma, prostate adenocarcinoma, seminoma, meningioma, mesothelioma, GI stromal tumor, liver cirrhosis, leiomyosarcoma, high-grade serous ovarian cancer, diverticulitis, acute appendicitis, metastatic melanoma, dedifferentiated liposarcoma | NIH U54 CA225088; NCI U2C CA233262; NCI U2C CA233280; Ludwig Center at Harvard Medical School and the Ludwig Cancer Research Foundation |
DOI:10.1101/2021.03.15.435473 | Restricted | SCR_021052 | Exemplar Microscopy Images of Tissues ( and Tumors) | 2026-02-14 02:04:09 | 3 | |||||
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Appyters Resource Report Resource Website 1+ mentions |
Appyters (RRID:SCR_021245) | software resource, web application | Collection of web-based software applications that enable users to execute bioinformatics workflows without coding. Turns Jupyter notebooks into fully functional standalone web-based bioinformatics applications. Each Appyter application introduces data entry form for uploading or fetching data, as well as for selecting options for various settings. Once user presses Submit, Appyter is executed in cloud and user is presented with Jupyter Notebook report that contain results. Report includes markdown text, interactive and static figures, and source code. Appyter users can share the link to the output report, as well as download the fully executable notebook for execution on other platforms. | Jupyter Notebooks, data-driven web apps collection, Jupyter Notebook results report |
is used by: Hypothesis Center has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24 CA224260; NHLBI U54 HL127624; NIH Office of the Director OT2 OD030160 |
DOI:10.1016/j.patter.2021.100213 | Free, Available for download, Freely available | https://github.com/MaayanLab/appyter https://github.com/MaayanLab/appyter-catalog |
SCR_021245 | 2026-02-14 02:04:12 | 9 | |||||||
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CNVpytor Resource Report Resource Website 10+ mentions |
CNVpytor (RRID:SCR_021627) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software Python package and command line tool for CNV/CNA analysis from depth of coverage by mapped reads. Software tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing. | Copy number variations, copy number alternations, whole genome sequencing, Python | has parent organization: Mayo Clinic | NCI U24 CA220242 | DOI:10.1101/2021.01.27.428472 | Free, Available for download, Freely available | SCR_021627 | 2026-02-14 02:04:40 | 19 | ||||||||
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Cumulus Resource Report Resource Website 1+ mentions |
Cumulus (RRID:SCR_021644) | data analysis software, software resource, data processing software, software application | Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. | Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data |
uses: Pegasus uses: Cirrocumulus uses: Pegasus-fus is listed by: Terra is related to: BICCN has parent organization: Broad Institute |
Klarman Cell Observatory ; Manton Foundation ; HHMI ; Ludwig Center at MIT ; Leidos Biomedical Research ; Frederick National Laboratory for Cancer Research ; NCI |
DOI:10.1038/s41592-020-0905-x | Free, Available for download, Freely available | https://app.terra.bio/#workspaces/kco-tech/Cumulus https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst |
SCR_021644 | 2026-02-14 02:04:19 | 2 | |||||||
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VAMPIRE Resource Report Resource Website 1+ mentions |
VAMPIRE (RRID:SCR_021721) | data processing software, data analysis software, software application, software resource, image analysis software | Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity. | cell morphology analysis, nuclear morphology analysis, fluorescence images, bright field images | NCI U54 CA143868; NCI R01 CA174388; NIA P30 AG021334; NIA U01 AG060903 |
DOI:10.1038/s41596-020-00432-x | Free, Available for download, Freely available | SCR_021721 | Visually Aided Morpho-Phenotyping Image Recognition | 2026-02-14 02:04:20 | 2 | ||||||||
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Motif Mutation Analysis for Regulatory Genomic Elements Resource Report Resource Website 500+ mentions |
Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) | MMARGE | data processing software, data analysis software, software toolkit, software application, software resource | Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation. | genome wide genetic variation, epigenetic data, identify collaborative transcription factor pairs, interpreting functional effects, non-coding genetic variation | NCI CA173903; NIGMS GM085764; NIDDK DK091183; NHLBI R00 123485 |
PMID:29893919 | Free, Available for download, Freely available | SCR_021902 | 2026-02-14 02:04:24 | 608 | ||||||||
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tximport Resource Report Resource Website 50+ mentions |
tximport (RRID:SCR_016752) | data analysis software, software resource, data processing software, software application | Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
SNSF 143883; European Commission ; NCI T32 CA009337 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/ https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html https://github.com/F1000Research/tximport https://bio.tools/tximport |
https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | tximport v1.4.0 | 2026-02-14 02:04:57 | 91 | ||||
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Polysolver Resource Report Resource Website 10+ mentions |
Polysolver (RRID:SCR_022278) | data analysis software, software resource, data processing software, software application | Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference. | HLA typing, whole exome sequencing data, accurate inference of germline alleles, high precision HLA-typing, alleles of class I HLA-A, B and C genes, detection of mutations, inferred alleles | has parent organization: Broad Institute | Blavatnik Family Foundation ; NHLBI 1RO1HL103532; NCI 1R01CA155010; AACR |
PMID:26372948 | Free, Available for download, Freely available | SCR_022278 | POLYmorphic loci reSOLVER, POLYSOLVER | 2026-02-14 02:04:42 | 30 |
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