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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NHGRI HG005998; NIGMS P50 GM071508 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-02-16 09:49:13 | 7 | ||||||||
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peddy Resource Report Resource Website 10+ mentions |
peddy (RRID:SCR_017287) | software application, data processing software, data analytics software, data analysis software, software resource | Software package that evaluates correspondence between stated sexes, relationships, and ancestries in pedigree file and those inferred from genotypes in VCF file resulting from human whole genome sequencing or whole exome sequencing studies. Facilitates both automated and interactive, visual detection of sample swaps, poor sequencing quality, and other indicators of sample problems. | sex, relation, ancestry, evaluate, pedigree, VCF file, genome, sequencing, exome, error, genotype | has parent organization: University of Utah; Utah; USA | NHGRI R01 HG006693 | PMID:28190455 | Free, Available for download, Freely available | http://quinlanlab.org/#portfolioModal8 | SCR_017287 | 2026-02-16 09:49:12 | 10 | |||||||
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E. coli Genome project Resource Report Resource Website 1+ mentions |
E. coli Genome project (RRID:SCR_008139) | database, data or information resource, topical portal, portal | The E. coli Genome Project has the goal of completely sequencing the E. coli and human genomes. They began isolation of an overlapping lambda clonebank of E. coli K-12 strain MG1655. Those clones served as the starting material in our initial efforts to sequence the whole genome. Improvements in sequencing technology have since reached the point where whole-genome sequencing of microbial genomes is routine, and the human genome has in fact been completed. They initiated additional sequencing efforts, concentrating on pathogenic members of the family Enterobacteriaceae -- to which E. coli belongs. They also began a systematic functional characterization of E. coli K-12 genes and their regulation, using the whole genome sequence to address how the over 4000 genes of this organism act together to enable its survival in a wide range of environments. | e. coli, enterobcteriaceae, gene, genome, human, journal aricle, knowledgebase, regulation, sequence, job | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | NIAID ; NHGRI |
nif-0000-20961 | SCR_008139 | E.Coli genome project | 2026-02-16 09:47:07 | 5 | ||||||||
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Bovine Genome Project Resource Report Resource Website |
Bovine Genome Project (RRID:SCR_008370) | Bovine Genome Project | data set, data analysis service, analysis service resource, production service resource, service resource, data or information resource | Downloadable files of the bos taurus genome. Draft assemblies available for download as contigs or linearized scaffolds of the genomic sequence of cow, Bos taurus, including the final draft assembly (7.1 coverage) and the two previous assemblies. The genome is sequenced to 6- to 8-fold sequence depth, with high-quality finished sequence in some areas. Accompanying EST and SNP analyses is also included. The bovine genome assembly and analysis and the study of cattle genetic history were published in April 24, 2009 issue of Science. The Human Genome Sequencing Center provides BLAST searches of the genome assemblies, either as contigs or as linearized chromosome sequences. The WGS sequence enriched BAC assemblies and the unassembled reads (sequencing reads that did not end up in the genome assembly) can also be searched by BLAST. Traces are available from the NCBI Trace Archive by using the link in the sidebar or by using NCBI MegaBLAST with a same species or cross species query. | bovine, cattle, cow, genome, genotype, reagent, sequencing, blast, genome assembly, contig, linearized chromosome, single nucleotide polymorphism, bac map, expressed sequence tag | has parent organization: Baylor University; Texas; USA | NHGRI ; USDA Agricultural Research Service ; USDA Cooperative State Research Education and Extension Service ; State of Texas ; Genome Canada ; Genome British Columbia ; CSIRO ; Agritech Investments Ltd. New Zealand ; Dairy Insight Inc. New Zealand ; AgResearch Ltd.New Zealand ; Robert J. Kleberg ; Jr. and Helen C. Kleberg Foundation ; National Texas and South Dakota Beef Check-off Funds |
PMID:19393050 | nif-0000-25603 | http://www.hgsc.bcm.tmc.edu/project-species-m-Bovine.hgsc?pageLocation=Bovine | SCR_008370 | 2026-02-16 09:47:10 | 0 | ||||||
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MGED Ontology Resource Report Resource Website 1+ mentions |
MGED Ontology (RRID:SCR_004484) | MO | ontology, data or information resource, controlled vocabulary | An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed. | microarray, biomaterial, treatment, mage, owl |
is listed by: BioPortal is related to: MIAME is related to: MIAME is related to: RNA Abundance Database has parent organization: Functional Genomics Data Society has parent organization: SourceForge |
NIBIB ; NHGRI P41HG003619 |
PMID:16428806 | nlx_47223 | http://purl.bioontology.org/ontology/MO | SCR_004484 | Microarray and Gene Expression Data Ontology | 2026-02-16 09:46:24 | 1 | |||||
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SO Resource Report Resource Website 10+ mentions |
SO (RRID:SCR_004374) | SO | ontology, data or information resource, controlled vocabulary | A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl. | annotation, sequence, biological sequence, sequence variation, genome, genome annotation, owl, FASEB list |
is listed by: BioPortal is related to: ASOoViR is related to: VAGrENT has parent organization: OBO has parent organization: Gene Ontology |
NHGRI HG02273 | PMID:20796305 PMID:20226267 PMID:18629179 PMID:15892872 |
The community can contribute to this resource | nlx_38918 | SCR_004374 | Sequence Ontology Project, Sequence Types and Features Ontology, Sequence Ontology | 2026-02-16 09:46:22 | 44 | |||||
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Velvet-SC Resource Report Resource Website 1+ mentions |
Velvet-SC (RRID:SCR_004377) | Velvet SC | software application, data processing software, sequence analysis software, data analysis software, software resource | Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria. | genome, single, cell, short, read, assembly |
is listed by: OMICtools is related to: Velvet has parent organization: University of California at San Diego; California; USA |
NHGRI R01 HG003647; Sloan Foundation ; NCRR P41 RR024851 |
PMID:21926975 | Free, Available for download, Freely available | OMICS_01504 | SCR_004377 | Velvet Single Cell | 2026-02-16 09:46:16 | 5 | |||||
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SMD Resource Report Resource Website 10+ mentions |
SMD (RRID:SCR_004987) | SMD | data analysis service, analysis service resource, data repository, database, storage service resource, production service resource, service resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 17, 2021. Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world. The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser. | data set, microarray, gene, image, gene expression, adenovirus disease, apoptosis, leukemia, source code, web service |
is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is related to: Longhorn Array Database is related to: Tuberculosis Database has parent organization: Princeton University; New Jersey; USA is parent organization of: SOURCE |
NCI ; Howard Hughes Medical Institute ; Stanford University School of Medicine; California; USA ; NHGRI R01 HG003469 |
PMID:18953035 PMID:17182626 PMID:15608265 PMID:12519956 PMID:11125075 |
Public, Open-source license, The community can contribute to this resource, Acknowledgement requested, THIS RESOURCE IS NO LONGER IN SERVICE | nlx_94141, OMICS_00870, r3d100010555 | https://doi.org/10.17616/R3DW40 | http://genome-www.stanford.edu/microarray/, http://smd.stanford.edu/ | SCR_004987 | Stanford Microarray Database | 2026-02-16 09:46:34 | 12 | |||
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FLASH Resource Report Resource Website 1000+ mentions |
FLASH (RRID:SCR_005531) | FLASh | software application, data processing software, sequence analysis software, data analysis software, software resource | Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: shovill is related to: CLIP-Explorer has parent organization: Johns Hopkins University; Maryland; USA |
NLM R01 LM006845; NIGMS R01 GM083873; NHGRI R01 HG006677 |
PMID:21903629 | Free, Available for download, Freely available | biotools:flash, OMICS_01047 | https://sourceforge.net/projects/flashpage/files/ https://bio.tools/flash https://sources.debian.org/src/flash/ |
SCR_005531 | Fast Length Adjustment of SHort reads, Fast Length Adjustment of Short reads | 2026-02-16 09:46:29 | 2175 | ||||
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Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome Resource Report Resource Website |
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) | HEFalMp | service resource, data or information resource, database | HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool. | human, map, gene, functional, pathway, disease, genomic, analysis, microarray, dna, protein, sequence | has parent organization: Princeton University; New Jersey; USA | New Jersey Commission on Cancer Research ; PhRMA Foundation 2007RSGl9572; NIGMS R01 GM071966; NSF DBI-0546275; NSF IIS-0513552; NHGRI T32 HG003284; NIGMS P50 GM071508 |
PMID:19246570 | nif-0000-37186 | SCR_003506 | Human Experimental / FunctionAL MaPper, Human Experimental/FunctionAL MaPper | 2026-02-16 09:46:02 | 0 | ||||||
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ArchR Resource Report Resource Website 100+ mentions |
ArchR (RRID:SCR_020982) | software application, data processing software, software toolkit, data analysis software, software resource | 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 | 2026-02-16 09:49:55 | 358 | ||||||||
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PhenStat Resource Report Resource Website 1+ mentions |
PhenStat (RRID:SCR_021317) | software application, data processing software, software toolkit, data analysis software, software resource | Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data. | Statistical analysis, phenotypic data, standardized analysis, bio.tools, Bioconductor |
is listed by: Bioconductor is listed by: bio.tools |
Wellcome Trust ; NHGRI U54 HG006370 |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | 2026-02-16 09:49:59 | 8 | ||||||
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LocusZoom.org Resource Report Resource Website 10+ mentions |
LocusZoom.org (RRID:SCR_021374) | data access protocol, software resource, web service | Web tool to investigate genome wide association results in their local genomic context. Adds new features to LocusZoom such as Manhattan plots, annotation options, and calculations that put findings in context. Used for interactive and embeddable visualization of genetic association study results.Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources. | Generate interactive plots, shareable plots, GWAS summary statistics, visualizing statistical genetic data, genetic association study | NHGRI HG009976; NIH BOEH15AMP |
DOI:10.1093/bioinformatics/btab186 | Free, Freely available | SCR_021374 | LocusZoom.js | 2026-02-16 09:50:00 | 32 | ||||||||
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CRISPResso Resource Report Resource Website 10+ mentions |
CRISPResso (RRID:SCR_021538) | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | Quantification, visualization, CRISPR-Cas9 outcomes, coding sequences evaluation, noncoding elements evaluation, selected off target sites evaluation, genome editing evaluation. | NHGRI RM1 HG009490; NIBIB R01 EB022376; NIGMS R35 GM118062; NIGMS R35 GM118158; NIDDK R03 DK109232; NHLBI P01 HL32262; NHGRI R00 HG008399; NIDDK P30 DK049216; NHLBI R01 HL119099; NHGRI R01 HG005085 |
PMID:27404874 PMID:30809026 |
Free, Available for download, Freely available | https://github.com/pinellolab/CRISPResso2 https://github.com/pinellolab/CRISPResso |
SCR_021538 | CRISPResso2 | 2026-02-16 09:50:04 | 21 | |||||||
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rtracklayer Resource Report Resource Website 10+ mentions |
rtracklayer (RRID:SCR_021325) | software resource, software toolkit | Software R package for interfacing with genome browsers.Supports integration of existing genome browsers with experimental data analyses performed in R. R interface to genome annotation files and UCSC genome browser. | Existing genome browsers integration, genome annotation files interface, interfacing with genome browsers | NHGRI P41 HG004059 | PMID:19468054 | Free, Available for download, Freely available | https://github.com/lawremi/rtracklayer | SCR_021325 | 2026-02-16 09:50:00 | 19 | ||||||||
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Adaptive Shrinkage in R Resource Report Resource Website 1+ mentions |
Adaptive Shrinkage in R (RRID:SCR_023486) | ashr | software resource, software toolkit | Software R package for adaptive shrinkage. Implements Empirical Bayes approach for large scale hypothesis testing and false discovery rate estimation. | adaptive shrinkage, large scale hypothesis testing, false discovery rate estimation, | NHGRI HG02585; Gordon and Betty Moore Foundation |
PMID:27756721 | Free, Available for download, Freely available | SCR_023486 | 2026-02-16 09:50:46 | 8 | ||||||||
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MR-PRESSO Resource Report Resource Website 50+ mentions |
MR-PRESSO (RRID:SCR_023697) | software resource, software toolkit | Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing. | Mendelian randomization, identify horizontal pleiotropic outliers, multi instrument summary level MR testing, | NIGMS R35 GM124836; NHLBI R01 HL139865; AstraZeneca ; Goldfinch Bio ; American Heart Association Cardiovascular Genome Phenome Discovery ; NIMH 1R01 MH094469; NIMH 1R01 MH107649; NHGRI 5U01 HG009088 |
PMID:29686387 | Free, Available for download, Freely available | SCR_023697 | Mendelian Randomization Pleiotropy RESidual Sum and Outlier | 2026-02-16 09:50:45 | 64 | ||||||||
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BioDepot-workflow-builder Resource Report Resource Website 1+ mentions |
BioDepot-workflow-builder (RRID:SCR_017402) | Bwb | data processing software, software application, software resource, workflow software | Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results. | bioinformatics, big, data, workflow, reproducible, Docker | NIGMS R01 GM126019; NHLBI U54 HL127624; NHGRI U24HG012674; NIAID R03AI159286 |
DOI:10.1016/j.cels.2019.08.007 | Free, Available for download, Freely available | SCR_017402 | 2026-02-16 09:49:14 | 1 | ||||||||
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StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | software application, data processing software, sequence analysis software, data analysis software, software resource | 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 | 2026-02-16 09:49:00 | 4072 | ||||||
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SVEngine Resource Report Resource Website 1+ mentions |
SVEngine (RRID:SCR_016235) | software application, data processing software, sequence analysis software, data analysis software, software resource, simulation software | Software for analysis and simulation of gene sequences and structural variants. This software works with FASTA, FASTQ, BAM, VAR, META, and NEWICK file formats. | structural, alteration, clonality, NGS, simulator, gene, allele, haplotype, variant | NHGRI R01 HG006137; CNSF 61370131 |
Free, Available to download | SCR_016235 | SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator | 2026-02-16 09:48:59 | 3 |
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