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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Minerva Resource Report Resource Website |
Minerva (RRID:SCR_024750) | Minerva | software application, data visualization software, data processing software, software resource | Software tools for interactive viewing and fast sharing of large image data. Comprises Minerva Author, a tool to create and annotate images, and Minerva Story, a narrative image viewer for web hosting. Used for interpreting and interacting with complex images, organized around guided analysis approach. Enables fast sharing of large image data that is stored on Amazon S3 and viewed using zoomable image viewer implemented using OpenSeadragon, making it ideal for integration into multi-omic browsers for data dissemination of tissue atlases. | tissue atlases, digital pathology, interactive viewing and sharing of large image data, data dissemination of tissue atlases, | has parent organization: Harvard University; Cambridge; United States | Gates ; NCI U54CA225088; NCI U2CCA233262; NCI U2C CA233280; Ludwig Cancer Center at Harvard ; NCI P30 CA06516 |
PMID:33768192 | Free, Freely available | https://www.cycif.org/software/minerva https://github.com/labsyspharm/minerva-story |
SCR_024750 | Minerva Author, Minerva Story | 2026-02-15 09:22:47 | 0 | |||||
|
scimap Resource Report Resource Website 10+ mentions |
scimap (RRID:SCR_024751) | software application, data visualization software, data processing software, software resource, software toolkit, data analysis software | Software toolkit for analyzing spatial molecular data. Underlying framework is generalizable to spatial datasets mapped to XY coordinates. Package uses anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. Python based implementation efficiently deals with large datasets of millions of cells. | Python, spatial single cell analysis, spatial datasets, analyzing spatial molecular data, | has parent organization: Harvard University; Cambridge; United States | NCI K99 CA256497 | Free, Available for download, Freely available | https://github.com/labsyspharm/scimap | SCR_024751 | 2026-02-15 09:23:38 | 10 | ||||||||
|
CRAPome Resource Report Resource Website 10+ mentions |
CRAPome (RRID:SCR_025008) | database, software resource, web service, data access protocol, data or information resource | Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions. | Mass Spectrometry contaminants, standardized negative controls, contaminant repository, AP-MS analysis, affinity purification, mass spectrometry data, | NIGMS 5R01GM94231; NIDA DP1DA026192; NHLBI HL112618-01; Canadian Institutes of Health Research ; government of Ontario ; Austrian Academy of Sciences ; Austrian Federal Ministry for Science and Research ; European Research Council ; Austrian Science Fund ; European Molecular Biology Organisation ; Netherlands Proteomics Center ; European Union 7th Framework Program ; Stowers Institute for Medical Research ; Human Frontier Science Program ; NCI R21 CA16006001A1 |
PMID:23921808 | Free, Freely available, | https://reprint-apms.org/ | SCR_025008 | CRAPome:Contaminant Repository for Affinity Purification | 2026-02-15 09:22:52 | 16 | |||||||
|
ReDU Resource Report Resource Website 1+ mentions |
ReDU (RRID:SCR_025105) | web service, data access protocol, software resource | Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE. | Mass Spectrometry data, find uniformly formatted public MS/MS data, formatted metadata, Global Natural Product Social Molecular Networking Platform, GNPS, find and re-analyze public Mass Spectrometry data, ReDU metadata standards, data validator, | has parent organization: University of California at San Diego; California; USA | NIGMS P41 GM103484; NCI R03 CA211211; NIGMS R01 GM107550; Sloan Foundation ; Gordon and Betty Moore Foundation ; American Society for Mass Spectrometry ; NSF ; Netherlands eScience Center ; FAPESP ; Krupp Endowed Fund ; US Office of Naval Research ; University of California ; San Diego Center for Microbiome Innovation SEED grants |
PMID:32807955 | Free, Freely available | SCR_025105 | Reanalysis of Data User | 2026-02-15 09:23:44 | 1 | |||||||
|
TooManyCells Resource Report Resource Website 1+ mentions |
TooManyCells (RRID:SCR_025328) | source code, software toolkit, software resource | Software suite of tools, algorithms, and visualizations focusing on relationships between cell clades. This includes new ways of clustering, plotting, choosing differential expression comparisons. Identifies and visualizes relationships of single-cell clades. | Spectral clustering, radial tree, visualization, cell clades, |
is related to: too-many-cells-python is related to: TooManyCellsInteractive |
NCI T32 CA009140; NCI R01 CA215518; NHLBI R01 HL145754; Sloan Foundation ; NCI R01 CA230800 |
PMID:32123397 | Free, Available for download, Freely available | https://gregoryschwartz.github.io/too-many-cells/ | SCR_025328 | 2026-02-15 09:23:50 | 4 | |||||||
|
glmpca Resource Report Resource Website 1+ mentions |
glmpca (RRID:SCR_025517) | source code, software toolkit, software resource | Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data. | dimension reduction, non-normally distributed data, principal components analysis, | NCI T32CA009337; NHGRI R00HG009007; Chan-Zuckerberg Initiative ; NHGRI R01HG005220; NIGMS R01GM083084; NHGRI P41HG004059 |
PMID:31870412 | Free, Available for download, Freely available, | https://CRAN.R-project.org/package=glmpca | SCR_025517 | generalized version of principal components analysis | 2026-02-15 09:23:53 | 1 | |||||||
|
CellMinerCDB Resource Report Resource Website 10+ mentions |
CellMinerCDB (RRID:SCR_025649) | web application, software resource | Web application integrating cancer cell line pharmacogenomics. Enables exploration and analysis of cancer cell line pharmacogenomic data across different sources. Focuses on cancer patient-derived human cell line molecular and pharmacological data. CellMinerCDB (v1.2) includes several improvements. | integrating cancer cell line pharmacogenomics, exploration and analysis of cancer cell line pharmacogenomic data, exploration and analysis, cancer cell line, pharmacogenomic data | is used by: National Cancer Institute Genomics and Pharmacology Core Facility | NIGMS P41 GM103504; NCI |
PMID:30553813 PMID:30553813 |
Free, Freely available, | SCR_025649 | , Cell Miner CDB, CellMiner Cross-Database, CellMinerCDB 1.2 | 2026-02-15 09:23:57 | 11 | |||||||
|
scRepertoire Resource Report Resource Website 50+ mentions |
scRepertoire (RRID:SCR_025691) | software toolkit, software resource | Software R toolkit for analyzing single-cell immune repertoire profiling. Used for single-cell immune receptor analysis. | single-cell immune receptor analysis, single-cell immune repertoire profiling, | NCI CA206255 | PMID:32789006 | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/scRepertoire.html | SCR_025691 | 2026-02-15 09:23:05 | 62 | ||||||||
|
UpSetR Resource Report Resource Website 50+ mentions |
UpSetR (RRID:SCR_026112) | source code, software toolkit, software resource | Software R package for visualization of intersecting sets and their properties. | visualization of intersecting sets, | NHGRI R00 HG007583; NHGRI U54HG007963; NCI U01 CA198935 |
PMID:28645171 | Free, Available for download, Freely available | https://cran.rstudio.com/web/packages/UpSetR/ | SCR_026112 | 2026-02-15 09:24:04 | 72 | ||||||||
|
AutoGVP Resource Report Resource Website 1+ mentions |
AutoGVP (RRID:SCR_026107) | software application, source code, software resource | Software tool integrates ClinVar variant annotation with modified InterVar classification approach, based on American College of Medical Genetics-Association for Molecular Pathology guidelines, to output germline variant classification. Since AutoGVP input only requires VCF file, it can facilitate large-scale, clinically focused classification of germline sequence variants. | germline variant classification, germline sequence variants, germline, sequence variants, | is related to: ClinVar | NCI R03CA230366; NCI R01CA237562; NCI R03CA287169 |
PMID:38426335 | Free, Available for download, Freely available | SCR_026107 | Automated Germline Variant Pathogenicity | 2026-02-15 09:24:04 | 3 | |||||||
|
NovoBreak Resource Report Resource Website 1+ mentions |
NovoBreak (RRID:SCR_026032) | software application, source code, software resource | Software tool to discover somatic and germline structural variation breakpoints in whole genome sequencing data. Can report accurate breakpoints of Deletions, Duplications, Inversions and Translocations. Designed for Illumina paired-end data. Local assembly for breakpoint detection in cancer genomes. | discover somatic and germline structural variation, structural variation breakpoints, whole-genome sequencing data, local assembly, breakpoint detection, cancer genomes, | NCI R01 CA172652; NHGRI U41 HG007497; NCI P30 CA016672 |
PMID:27892959 | Free, Available for download, Freely available, | SCR_026032 | 2026-02-15 09:24:03 | 1 | |||||||||
|
OncoTree Resource Report Resource Website 10+ mentions |
OncoTree (RRID:SCR_026218) | data or information resource, topical portal, disease-related portal, portal | Community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research. Cancer classification system for precision oncology. | cancer classification platform, rare and common cancers, cancer classification, precision oncology, | cancer | NCI P30 CA008748 | PMID:33625877 | Free, Freely available | SCR_026218 | 2026-02-15 09:24:01 | 14 | ||||||||
|
AACR GENIE cBioPortal Resource Report Resource Website 10+ mentions |
AACR GENIE cBioPortal (RRID:SCR_026217) | organization portal, portal, consortium, data or information resource | International data-sharing consortium focused on generating an evidence base for precision cancer medicine by integrating clinical-grade cancer genomic data with clinical outcome data of cancer patients treated at multiple institutions worldwide. | International data-sharing consortium, generating an evidence base, precision cancer medicine, integrating clinical-grade cancer genomic data, clinical outcome data, cancer patients, | NCI CA008748; Howard Hughes Medical Institute ; NCI 5U01CA168394; NCI 5P50CA098258; NCI 5P50CA083639; NHGRI U54HG008100; NCI U24CA210950; NCI U24CA209851; NCI 2P30CA006516; NCI 5P30CA068485; NCI CA006973; NCI CA121113; NCI CA180950 |
PMID:28572459 | Restricted | SCR_026217 | 2026-02-15 09:23:58 | 13 | |||||||||
|
Strainy Resource Report Resource Website |
Strainy (RRID:SCR_026430) | software application, source code, software resource | Software tool for phasing and assembly of bacterial strains from long-read sequencing data (either Oxford Nanopore or PacBio). Given reference (or collapsed de novo assembly) and set of aligned reads as input, tool produces multi-allelic phasing, individual strain haplotypes and strain-specific variant calls. Used for phasing and assembly of strain haplotypes from long-read metagenome sequencing. | phasing and assembly, strain haplotypes, long-read metagenome sequencing, | NCI | PMID:39327484 | Free, Available for download, Freely available | SCR_026430 | 2026-02-15 09:23:16 | 0 | |||||||||
|
xCell Resource Report Resource Website 50+ mentions |
xCell (RRID:SCR_026446) | web application, source code, software toolkit, software resource | Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis. | Cell types enrichment analysis, cell type, enrichment analysis, generating cell type scores and R scripts, development of xCell, | Gruss Lipper Postdoctoral Fellowship ; NCI U24 CA195858; NIAID |
PMID:29141660 | Free, Available for download, Freely available | http://xCell.ucsf.edu/ | SCR_026446 | 2026-02-15 09:24:12 | 62 | ||||||||
|
PathoMAN Resource Report Resource Website |
PathoMAN (RRID:SCR_026552) | PathoMAN | web application, software resource | Web application to automate germline genomic variant curation from clinical sequencing based on ACMG guidelines. Aggregates multiple tracks of genomic, protein and disease specific information from public sources. | Aggregates multiple tracks, automate germline genomic variant curation, clinical sequencing, genomic, protein, disease specific information, public sources, | NCI R21CA029533; NCI P50CA221745; NCI P30CA008748 |
PMID:30787465 | Free, Freely available, | SCR_026552 | Pathogenicity of Mutation Analyzer | 2026-02-15 09:24:03 | 0 | |||||||
|
NetworkDataCompanion Resource Report Resource Website 1+ mentions |
NetworkDataCompanion (RRID:SCR_026532) | software library, source code, software toolkit, software resource | Software R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo. Streamlines routine steps in TCGA data processing, including filtering and mapping gene and sample identifiers between modalities and allows modality-specific data transformation, such as normalization and cleaning. | TCGA and GTEx data analysis, TCGA data processing, filtering and mapping gene, normalization and cleaning, | NCI R35CA220523; NCI U24CA231846; NCI P50CA127003; NHGRI R01HG011393; NHGRI R01HG125975; NHLBI P01HL114501; NHLBI T32HL007427; NHLBI K01HL166376; American Lung Association |
PMID:39574772 | Free, Available for download, Freely available | SCR_026532 | 2026-02-15 09:24:13 | 1 | |||||||||
|
Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | source code, software toolkit, software resource | Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences. | Borzoi models access, convolutional neural networks, predict RNA-seq coverage, | Common Fund of the Office of the Director ; NCI ; NHGRI ; NHLBI ; NIDA ; NIMH ; NINDS |
PMID:39779956 | Free, Available for download, Freely available | SCR_026619 | 2026-02-15 09:24:01 | 1 | |||||||||
|
PEtab Resource Report Resource Website |
PEtab (RRID:SCR_026915) | source code, software resource | Repository contains PEtab specifications and additional documentation. Data format for specifying parameter estimation problems in systems biology. SBML and TSV based data format for parameter estimation problems in systems biology. Human- and computer- readable format for representing parameter estimation problems in systems biology. | SBML, TSV, data format, parameter estimation problems, systems biology, specifying parameter estimation problems, | European Unions Horizon 2020 ; NCI U54 CA225088 |
PMID:33497393 | Free, Available for download, Freely available | https://github.com/PEtab-dev/PEtab https://zenodo.org/records/3732958 |
SCR_026915 | 2026-02-15 09:23:26 | 0 | ||||||||
|
SigProfilerAssignment Resource Report Resource Website 1+ mentions |
SigProfilerAssignment (RRID:SCR_026899) | software application, source code, software resource | Software tool for assignment of known mutational signatures to individual samples and individual somatic mutations. | assignment of known mutational signatures, individual samples, individual somatic mutations, | Cancer Research UK Grand Challenge Award ; NIEHS R01ES030993; NIEHS R01ES032547; NCI R01CA269919; Packard Fellowship for Science and Engineering |
PMID:37502962 | Free, Available for download, Freely available, | SCR_026899 | 2026-02-15 09:24:15 | 3 |
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.
