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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Exemplar Microscopy Images of Tissues Resource Report Resource Website 1+ mentions |
Exemplar Microscopy Images of Tissues (RRID:SCR_021052) | EMIT | 2d spatial image, data or information resource, data repository, data set, experimental protocol, image, image collection, image repository, immuno detection protocol, immunofluorescence, narrative resource, service resource, storage service 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 | Ludwig Center at Harvard Medical School and the Ludwig Cancer Research Foundation ; NCI U2C CA233262; NCI U2C CA233280; NIH U54 CA225088 |
DOI:10.1101/2021.03.15.435473 | Restricted | SCR_021052 | Exemplar Microscopy Images of Tissues ( and Tumors) | 2026-09-05 06:29:33 | 3 | |||||
|
Appyters Resource Report Resource Website 10+ 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 | 2026-09-05 06:29:37 | 16 | |||||||
|
CNVpytor Resource Report Resource Website 10+ mentions |
CNVpytor (RRID:SCR_021627) | data analysis software, data processing software, sequence 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 | 2026-09-05 06:29:43 | 24 | ||||||||
|
Cumulus Resource Report Resource Website 1+ mentions |
Cumulus (RRID:SCR_021644) | data analysis software, data processing software, software application, software resource | 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 |
Frederick National Laboratory for Cancer Research ; HHMI ; Klarman Cell Observatory ; Leidos Biomedical Research ; Ludwig Center at MIT ; Manton Foundation ; 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 | 2026-09-05 06:29:43 | 3 | |||||||
|
VAMPIRE Resource Report Resource Website 1+ mentions |
VAMPIRE (RRID:SCR_021721) | data analysis software, data processing software, image analysis software, software application, software resource | 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 R01 CA174388; NCI U54 CA143868; 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 | 2026-09-05 06:29:45 | 2 | ||||||||
|
TIMER Resource Report Resource Website 1000+ mentions |
TIMER (RRID:SCR_018737) | TIMER | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | 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 | Dana-Farber Cancer Institute ; National Natural Science Foundation of China ; NCI CA180980 |
PMID:29092952 | Free, Freely available | SCR_018737 | Tumor IMmune Estimation Resource | 2026-09-05 06:28:41 | 3010 | |||||||
|
ROSIE Resource Report Resource Website 10+ mentions |
ROSIE (RRID:SCR_018764) | ROSIE | application programming interface, data access protocol, software resource, 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 | Howard Hughes Medical and Institute International Student Research Fellowship ; NCI U54 CA143907; NCRR R00 RR024107; NEI PN2 EY016586; NIGMS R01 GM073151; NIGMS R01 GM07822; NIGMS R21 GM102716; NIGMS T32 GM 88118; NSF ; Taiwan Governmental Scholarship for Study Abroad |
PMID:23717507 | Restricted | https://rosie.rosettacommons.org/ | SCR_018764 | Rosetta Online Server that Includes Everyone | 2026-09-05 06:28:42 | 10 | |||||
|
CAIRN Resource Report Resource Website |
CAIRN (RRID:SCR_019101) | data access protocol, data processing software, data visualization software, software application, software resource, web service | 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 | NCI CA102310; NCI CA107263; NCI CA177519; NCI CA207729; NCI P30 CA138313; NIA AG033082; NIGMS GM132055; Nine Girls Ask Foundation |
PMID:31923184 | Free, Available for download, Freely available | https://github.com/jrdelaney/CAIRN | SCR_019101 | Copy Alterations Intuitive Rendering Navigator | 2026-09-05 06:28:46 | 0 | |||||||
|
Phenograph Resource Report Resource Website 100+ mentions |
Phenograph (RRID:SCR_016919) | PhenoGraph | data analysis software, data processing software, software application, software resource | Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity. | high, dimention, single, cell, data, phenotype, analysis, heterogeneity |
uses: Python Programming Language is related to: Rphenograph |
CIRM DR1 01477; CIRM RB201592; Entertainment Industry Foundation ; NCI P01 CA034233; NCI R01 CA130826; NCI R01 CA164729; NCI U54 CA121852; NCI U54 CA143907; NCI U54 CA149145; NIAID U19 AI057229; NICHD DP1 HD084071; NIGMS R00 GM104148; NIH Office of the Director DP2 OD002414; NIH N01 HV00242; Packard Fellowship for Science and Engineering ; Rachford and Carlota Harris Endowed Professorship ; Stand Up To Cancer Phillip A. Sharp Award SU2CAACRPS04; US Department of Health and Human Services HHSN272200700038C; US DOD W81XWH1210591; US FDA HHSF223201210194C |
PMID:26095251 | Free, Available for download, Freely available | https://github.com/JinmiaoChenLab/Rphenograph | https://github.com/jacoblevine/PhenoGraph | SCR_016919 | 2026-09-05 06:28:15 | 235 | |||||
|
ImmuneDB Resource Report Resource Website 1+ mentions |
ImmuneDB (RRID:SCR_017125) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | 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 | NCI P30 CA016520; NIAID P01 AI106697; NIAID P30 AI0450080; NIDDK UC4 DK112217 |
PMID:30298069 | Free, Available for download, Freely available | https://github.com/arosenfeld/immunedb | SCR_017125 | 2026-09-05 06:28:19 | 8 | |||||||
|
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 | 2026-09-05 06:28:19 | 0 | ||||||||||
|
exRNA Atlas Resource Report Resource Website 10+ mentions |
exRNA Atlas (RRID:SCR_017221) | analysis service resource, application programming interface, atlas, consortium, controlled vocabulary, data access protocol, data analysis service, data or information resource, data repository, database, expression atlas, ontology, organization portal, portal, production service resource, service resource, software resource, storage service resource | 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 | American Cancer Society ResearchProfessor Award ; Frank McGraw Memorial Chair in CancerResearch ; NCATS UH3 TR000906; NCATS UH3 TR000943; NCI CA217685; NCI R01 CA163849; NCI R35 CA209904; NCI U19 CA179512; NHLBI K23 HL127099; NHLBI R01 HL122547; NHLBI R01 HL136685; NIA R01 AG059729; NIDA U54 DA036134; NIDDK P30 DK63720; NIGMS R25 GM056929 |
PMID:30951672 | Restricted | SCR_017221 | 2026-09-05 06:28:20 | 29 | |||||||
|
GenePattern Notebook Resource Report Resource Website 1+ mentions |
GenePattern Notebook (RRID:SCR_015699) | electronic laboratory notebook, software application, software resource, systems interoperability software, web application | Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code. | gene, genomics research, research narrative, notebook system, analysis notebook, bio.tools |
is listed by: bio.tools is listed by: Debian is affiliated with: GenePattern |
NIGMS R01-GM074024; NCI U24-CA194107 |
PMID:28822753 | Open Source, Free, Available for download, Account required | biotools:GenePattern_notebook | https://bio.tools/GenePattern_notebook | SCR_015699 | GenePattern Notebook environment | 2026-09-05 06:27:58 | 3 | |||||
|
TISSUES Resource Report Resource Website 10+ mentions |
TISSUES (RRID:SCR_015665) | data or information resource, database, software resource, web application | Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. | tissue expression, proteomic, transcriptomic, text-mining, brenda tissue ontology, protein identifier, bio.tools |
uses: BRENDA Tissue and Enzyme Source Ontology is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation NNF14CC0001; NCI U54 CA189205-01; CSIRO’s OCE Science Leader program |
PMID:26157623 | Freely available, Free, Available for download | biotools:tissues | https://bio.tools/tissues | SCR_015665 | TISSUES: Tissue Expression Database, Tissue Expression Database | 2026-09-05 06:27:57 | 45 | |||||
|
LINCS Joint Project - Breast Cancer Network Browser Resource Report Resource Website 1+ mentions |
LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) | LJP-BCNB, LJP, BCNB | data access protocol, service resource, software resource, web service | Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations. | breast, cancer, tissue, cluster, drug, perturbation, cell, line, gene, expression |
is related to: L1000 Characteristic Direction Signature Search Engine is related to: LINCS Project |
Breast cancer | NCI U54 CA189201; NHGRI U54 HG006093; NHLBI U54 HL127365; NHLBI U54 HL127624 |
PMID:29084964 | Free, Freely available | https://github.com/MaayanLab/LJP | SCR_016181 | LINCS Joint Project, Breast Cancer Network Browser | 2026-09-05 06:28:05 | 1 | ||||
|
SnapATAC Resource Report Resource Website 10+ mentions |
SnapATAC (RRID:SCR_020981) | data analysis software, data processing software, software application, software resource, software toolkit | 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; NIMH U19 MH114831; UCSD School of Medicine |
PMID:33637727 | Free, Available for download, Freely available | https://github.com/r3fang/SnapATAC | SCR_020981 | Single Nucleus Analysis Pipeline for ATAC-seq | 2026-09-05 06:29:32 | 23 | |||||||
|
SV-plaudit Resource Report Resource Website 1+ mentions |
SV-plaudit (RRID:SCR_016285) | data analysis software, data processing software, image analysis software, software application, software resource | Software for rapidly curating structural variant (SVs) predictions. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis. | genomics, structural, variants, visualization, manual, curation, prediction, image, alignment | NCI U24 CA209999; NHGRI K99 HG009532; NHGRI R01 HG006693; NIGMS R01 GM124355 |
Free, Available for download | SCR_016285 | 2026-09-05 06:28:06 | 2 | ||||||||||
|
Drug Gene Budger Resource Report Resource Website |
Drug Gene Budger (RRID:SCR_016489) | DGB | data access protocol, service resource, software resource, web service | Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures. | identify, drug, small, molecule, predict, influence, expression, mammalian, gene, regulate, target |
is related to: LINCS Project has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA works with: CMAP works with: Gene Expression Omnibus (GEO) |
BD2K-LINCS Data Coordination and Integration Center Mount Sinai Knowledge Management Center for IDG ; NCI U24 CA224260; NHLBI U54 HL127624 |
PMID:30169739 | Restricted | SCR_016489 | Drug Gene Budger | 2026-09-05 06:28:09 | 0 | ||||||
|
Spectroscopic Imaging, VIsualization, and Computing (SIVIC) Resource Report Resource Website 1+ mentions |
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 P01 CA11816; NCI RO1 CA127612; NIBIB P41EB013598 |
PMID:23970895 | Free, Available for download, Freely available | SCR_027875 | 2026-09-05 06:36:01 | 2 | ||||||||
|
tximeta Resource Report Resource Website 1+ mentions |
tximeta (RRID:SCR_028005) | software resource, software toolkit | Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility. | reference sequence checksums, provenance identification in RNA-seq, numerous annotation, metadata gathering, | NCI P01 CA142538; NHGRI R01 HG009937; NHGRI U41 HG004059; NIEHS P30 ES010126; NIMH R01 MH118349 |
PMID:32097405 | Free, Available for download, Freely available | SCR_028005 | Tximeta | 2026-09-05 06:36:04 | 1 |
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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
