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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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cBioPortal Resource Report Resource Website 5000+ mentions |
cBioPortal (RRID:SCR_014555) | data or information resource, database, portal | A portal that provides visualization, analysis and download of large-scale cancer genomics data sets. | cancer, genomics, database, portal, data sets, FASEB list | is used by: NaviCom | NCI U24CA143840; NCRR RR031228-02 |
PMID:23550210 PMID:22588877 |
Please cite, Software is available via GitHub, Open source | https://github.com/cBioPortal/cbioportal/ https://github.com/cBioPortal/cbioportal/blob/master/docs/README.md | SCR_014555 | cBioPortal for Cancer Genomics | 2026-02-15 09:21:04 | 8539 | ||||||
|
liftOver Resource Report Resource Website 500+ mentions |
liftOver (RRID:SCR_018160) | software application, service resource, data processing software, software resource | Web tool to convert genome coordinates and genome annotation files between assemblies. Used to translate genomic coordinates from one assembly version into another and retrieves putative orthologous regions in other species using UCSC chained and netted alignments. | Convert genome coordinate, genome annotation file, translate genomic coordinate, assembly version, retrieve orthologous region |
is related to: UCSC Genome Browser has parent organization: University of California at Santa Cruz; California; USA |
NHGRI ; Howard Hughes Medical Institute ; NCI |
DOI:10.1093/nar/gkj144 | Free, Available for download, Freely available | SCR_018160 | 2026-02-15 09:22:11 | 762 | ||||||||
|
GeoDa Resource Report Resource Website 100+ mentions |
GeoDa (RRID:SCR_018559) | software application, data visualization software, data processing software, software resource, data analysis software | Software program for spatial analysis for non geographic information systems specialists. Includes functionality ranging from simple mapping to exploratory data analysis, visualization of global and local spatial autocorrelation, and spatial regression. | Spatial analysis, data analysis, spatial autocorrelation visualization, spatial regression, mapping | NSF BCS 9978058; NCI R01 CA95949 |
DOI:10.1111/j.0016-7363.2005.00671.x | Free, Freely available | SCR_018559 | 2026-02-15 09:21:39 | 192 | |||||||||
|
FairSubset Resource Report Resource Website |
FairSubset (RRID:SCR_019102) | web service, data access protocol, software resource | Web tool to choose representative subsets of data for use with replicates or groups of different sample sizes. Used to retain distribution information at single datum level and may be considered for standardized use in fair publishing practices. | Representative data subsets, different sample sizes groups, different sample sizes replicates, retaining distribution information, fair publishing | NCI CA207729; Polish government grant |
PMID:31583263 | Free, Freely available | SCR_019102 | 2026-02-15 09:22:19 | 0 | |||||||||
|
GSVA Resource Report Resource Website 100+ mentions |
GSVA (RRID:SCR_021058) | GSVA | software application, data processing software, software resource, software toolkit, data analysis software | Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner. | Gene set enrichment, variation estimation, pathway activity, sample population, microarray, RNA-seq, data analysis | is listed by: Bioconductor | ISCIII COMBIOMED ; Spanish MINECO ; NCI U54 CA149237 |
PMID:23323831 | Free, Available for download, Freely available | SCR_021058 | Gene Set Variation Analysis | 2026-02-15 09:22:31 | 256 | ||||||
|
CyLinter Resource Report Resource Website 1+ mentions |
CyLinter (RRID:SCR_021157) | software application, data processing software, software resource, segmentation software, image analysis software | Open source software tool as interactive image segmentation filter for multiplex microscopy that aids in identification and removal of cell segmentation instances corrupted by optical and image processing artifacts. | multiplex microscopy, quality control, single-cell data, Interactive Image Segmentation Filter | NCI U2C CA233262; NCI U54 CA225088 |
Free, Available for download, Freely available | SCR_021157 | 2026-02-15 09:22:26 | 3 | ||||||||||
|
ArchR Resource Report Resource Website 100+ mentions |
ArchR (RRID:SCR_020982) | software application, data processing software, software resource, software toolkit, data analysis software | Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing. | single-cell ATAC-seq data analysis, single-cell ATAC-seq data processing, single cell chromatin accessibility analysis, doublet removal, single cell clustering, cell type identification, unified peak set generation, cellular trajectory identification, transcription factor footprinting | NHGRI RM1 HG007735; NHGRI UM1 HG009442; NCI R35 CA209919; NHGRI UM1 HG009436; NCI U2C CA233311; NIAID U19 AI057266; NIA K99 AG059918; American Society of Hematology Scholar Award ; International Collaborative Award ; Defense Advanced Research Project Agency ; Ray and Dagmar Dolby Family Fund ; Stanford Cancer Institute-Goldman Sachs Foundation Cancer Research Award |
PMID:33633365 | Free, Available for download, Freely available | https://github.com/GreenleafLab/ArchR https://www.archrproject.com/ https://github.com/GreenleafLab/ArchR_2020 |
SCR_020982 | 2026-02-15 09:22:24 | 358 | ||||||||
|
MCMICRO Resource Report Resource Website 10+ mentions |
MCMICRO (RRID:SCR_021048) | software application, image processing software, data processing software, software resource | Open source software tool as multiple choice microscopy pipeline for multiplexed whole slide imaging and tissue microarrays. Scalable, modular image processing pipeline for multiplexed tissue imaging. Used for performing sequential steps needed to transform large, multi channel whole slide images into single cell data. | NCI U54 CA225088; Harvard Medical School ; Ludwig Cancer Research Foundation ; University of Zurich BioEntrepreneur Fellowship ; Swiss National Science Foundation Early Postdoc Mobility fellowship |
DOI:10.1101/2021.03.15.435473 | Free, Available for download, Freely available | https://github.com/labsyspharm/mcmicro | SCR_021048 | 2026-02-15 09:22:24 | 11 | |||||||||
|
StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
the Cancer Prevention and Research Institute of Texas ; NHGRI R01 HG006677; NIGMS R01 GM105705; NHGRI R01 HG006102; NCI R01 CA120185; NCI R01 CA134292 |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie https://bio.tools/stringtie https://sources.debian.org/src/stringtie/ |
SCR_016323 | 2026-02-15 09:21:38 | 4072 | ||||||
|
DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | software tool, software application, data processing software, software resource, data analysis software | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337; European Union’s 7th Framework Programme |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2 https://bio.tools/deseq2 |
SCR_015687 | 2026-02-15 09:21:36 | 43994 | |||||||
|
Differential Gene Correlation Analysis Resource Report Resource Website 1+ mentions |
Differential Gene Correlation Analysis (RRID:SCR_020964) | DGCA | software application, data processing software, data analysis software, software resource | Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix. | Differential gene, gene, gene correlation, correlation analysis, input matrices, differential correlations, identifier pairs, gene expression data, calculate differential correlations | is listed by: CRAN | NIA F30 AG052261; NIA R01 AG046170; NCI R01 CA163772; NIAID U01 AI111598 |
PMID:27846853 | Free, Available for download, Freely available | https://github.com/andymckenzie/DGCA | SCR_020964 | 2026-02-15 09:22:30 | 1 | ||||||
|
Markov Affinity based Graph Imputation of Cells Resource Report Resource Website 50+ mentions |
Markov Affinity based Graph Imputation of Cells (RRID:SCR_022371) | MAGIC | software application, data processing software, data analysis software, software resource | Software tool for imputing missing values restoring structure of large biological datasets.Method that shares information across similar cells, via data diffusion, to denoise cell count matrix and fill in missing transcripts. | imputing missing values, restoring structure, shares information across similar cells, denoise cell count matrix, fill in missing transcripts | NICHD DP1 HD084071; NCI R01 CA164729; NCI P30 CA008748; American Cancer Society ; Simons SFARI grants |
PMID:29961576 | Free, Available for download, Freely available | SCR_022371 | 2026-02-15 09:22:52 | 83 | ||||||||
|
Minimum Information about Tissue Imaging Resource Report Resource Website |
Minimum Information about Tissue Imaging (RRID:SCR_022830) | MITI | organization portal, portal, consortium, data or information resource, narrative resource, standard specification | Consortium provides guidelines for highly multiplexed tissue images. Standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology. Data and metadata standards consistent with Findable, Accessible, Interoperable, and Reusable (FAIR) standards that guide data deposition, curation and release. | Data and metadata standards, FAIR, tissue imaging, minimum information standard, guidelines for highly multiplexed tissue images | NCI U2C CA233262; NCI U54 CA225088; NCI U2C CA233280; NCI U2C CA233195; NCI U2C CA233291; NCI U2C CA233311; NCI U2C CA233238; NCI U2C CA233285; NCI U2C CA233303; NCI U2C CA233284; NCI U2C CA233254 |
PMID:35277708 | Free, Freely available | https://github.com/miti-consortium/MITI | SCR_022830 | MITI Consortium | 2026-02-15 09:22:20 | 0 | ||||||
|
miQC Resource Report Resource Website 1+ mentions |
miQC (RRID:SCR_022697) | software application, data processing software, data analysis software, software resource | Software tool as flexible, probablistic metrics for quality control of scRNA-seq data. Adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. Data driven QC metric that jointly models proportion of reads mapping to mtDNA and number of detected genes with mixture models in probabilistic framework to predict which cells are low quality in given dataset. | scRNA-seq data quality control, QC metric, low quality data prediction, single cell RNA-sequencing data | NCI CA237170; NHGRI HG009007; European Union Horizon 2020 research and innovation program ; Academy of Finland ; Cancer Foundation Finland |
PMID:34428202 | Free, Available for download, Freely available | SCR_022697 | 2026-02-15 09:22:56 | 2 | |||||||||
|
Stitchr Resource Report Resource Website 1+ mentions |
Stitchr (RRID:SCR_022139) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information. | Stitch together coding TCR nucleotide sequences, Python, T cell receptors nucleotide, V and J gene symbols, hypervariable CDR3 amino acid sequence, fully spliced TCR cDNA | NCI R01 CA164273; NIAID R43 AI120313; NCI R43 CA232942; Emily Venanzi Fund |
PMID:35325179 | Free, Available for download, Freely available | SCR_022139 | 2026-02-15 09:22:12 | 3 | |||||||||
|
Physician Data Query Resource Report Resource Website 1+ mentions |
Physician Data Query (RRID:SCR_006833) | PDQ | clinical trial, database, ontology, people resource, registry, data or information resource, controlled vocabulary | NCI''s comprehensive cancer database that contains summaries on a wide range of cancer topics; a registry of 8,000+ open and 19,000+ closed cancer clinical trials from around the world; a directory of professionals who provide genetics services; the NCI Dictionary of Cancer Terms, with definitions for 6,800+ cancer and medical terms; and the NCI Drug Dictionary, which has information on 2,300+ agents used in the treatment of cancer or cancer-related conditions. The PDQ cancer information summaries are peer reviewed and updated monthly by six editorial boards comprised of specialists in adult treatment, pediatric treatment, supportive care, screening and prevention, genetics, and complementary and alternative medicine. The Boards review current literature from more than 70 biomedical journals, evaluate its relevance, and synthesize it into clear summaries. Many of the summaries are also available in Spanish. | adult, pediatric, child, alternative, breast, clinical trial, colorectal, hypercalcemia, legal, lung, medicine, medullary, nausea, ovarian, pain, pathophysiology, pediatric, pharmaceutical, physician, prevention, prognosis, prostate, psychosocial, query, risk factor, screening, social, syndrome, thyroid, treatment, umls, genetics, medical, drug, peer review |
is listed by: BioPortal has parent organization: National Cancer Institute |
Cancer, Cancer-related condition | NCI | nif-0000-21318 | SCR_006833 | PDQ - NCI''s Comprehensive Cancer Database | 2026-02-15 09:19:20 | 2 | ||||||
|
Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | database, service resource, storage service resource, data repository, data or information resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934 https://doi.org/10.48550/arxiv.1506.00272 https://doi.org/10.7303/ https://dx.doi.org/10.7303 https://doi.org/10.17616/R3B934 |
SCR_006307 | 2026-02-15 09:19:12 | 1002 | |||||
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Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | web service, data access protocol, software resource | Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations. | Ranking, gene, arbitrary, text, query, list, predict, association, data, integration, interactive, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | 2026-02-15 09:22:09 | 4 | ||||||
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Structure Harvester Resource Report Resource Website 100+ mentions |
Structure Harvester (RRID:SCR_017636) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web based program for collating results generated by program STRUCTURE. Provides assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of number of genetic groups that best fit data. Reformats data for use in downstream programs, such as CLUMPP.It is complement for using software Structure in genetics population. Website and program for visualizing STRUCTURE output and implementing Evanno method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Visualizing, STRUCTURE, Evanno, method, collating, result, detection, genetic, group, fit, data, reformat |
is related to: University of California at Santa Cruz; California; USA is related to: University of California at Irvine; California; USA is related to: University of California at Los Angeles; California; USA works with: STRUCTURE |
NCI U24 CA143858; NCI R21 CA135937 |
DOI:10.1007/s12686-011-9548-7 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017636 | StructureHarvester | 2026-02-15 09:22:05 | 297 | |||||||
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Interactive Line Graph Resource Report Resource Website |
Interactive Line Graph (RRID:SCR_018334) | data analysis service, software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions. | Line graph, scientific publication, summary statistics, examine lines, time point, changes between time points, data, statistic, plot | NCI P50 AG44170; Office of Research on Women Health |
PMID:27332507 | Free, Freely available | SCR_018334 | 2026-02-15 09:22:20 | 0 |
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