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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Preseq Resource Report Resource Website 10+ mentions |
Preseq (RRID:SCR_018664) | software application, data processing software, software resource, software toolkit, data analysis software | Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries. | Genome, high throughput sequencing, predicting library complexity, distinct yield prediction, genomic library, initial sequencing experiment, molecular complexity prediction, sequencing libraryb, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:23435259 | Free, Freely available | biotools:preseq | https://github.com/smithlabcode/preseq https://bio.tools/preseq |
SCR_018664 | 2026-02-15 09:21:40 | 19 | |||||||
|
EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | database, software resource, data access protocol, web service, data or information resource | Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. | Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Warwick; Coventry; United Kingdom |
Biotechnology and Biological Sciences Research Council ; Wellcome Trust |
Restricted | biotools:Enterobase | https://bio.tools/EnteroBase | SCR_019019 | 2026-02-15 09:22:26 | 233 | |||||||
|
Differential Methylation Analysis Package Resource Report Resource Website |
Differential Methylation Analysis Package (RRID:SCR_019148) | DMAP | software application, data processing software, software resource, software toolkit, data analysis software | Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity. | Genomic DNA methylation, DNA methylation analysis, bisulphite sequenced data, reference methylomes generation, genome, aligned SAM files processing, differentially methylated regions | has parent organization: University of Otago; Dunedin; New Zealand | National Centre for Growth and Development and Health Research Council ; New Zealand |
PMID:24608764 | Free, Freely available | SCR_019148 | 2026-02-15 09:22:20 | 0 | |||||||
|
Encode Resource Report Resource Website 1000+ mentions |
Encode (RRID:SCR_015482) | organization portal, portal, data set, consortium, data or information resource | Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present. | genome, sequencing, protein, rna, dna, consortium |
is related to: modENCODE is related to: ENCODE is related to: 3D Genome has parent organization: Stanford University; Stanford; California has parent organization: University of California at Santa Cruz; California; USA |
NHGRI HG006992 | PMID:15499007 | Free, Freely available | SCR_015482 | ENCODE Project | 2026-02-15 09:21:17 | 1244 | |||||||
|
BECA Resource Report Resource Website 1+ mentions |
BECA (RRID:SCR_015846) | BECA | software application, data visualization software, data processing software, software resource, image analysis software | Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version. | visual exploration, brain, neuroscience, network, genetic determinant, fmri, neuroimaging, genome | has parent organization: Indiana University School of Medicine; Indiana; USA | NLM R01 LM011360; NIA U01 AG024904; NIA RC2 AG036535; NIA R01 AG19771; NIA P30 AG10133; NSF IIS-1117335; NIBIB R01 EB022574 |
PMID:27171688 | Free, Available for download | SCR_015846 | Brain Explorer for Connectome Analysis (BECA), BECA - Brain Explorer for Connectome Analysis | 2026-02-15 09:21:25 | 5 | ||||||
|
Alliance of Genome Resources Resource Report Resource Website 50+ mentions |
Alliance of Genome Resources (RRID:SCR_015850) | organization portal, portal, service resource, consortium, data or information resource, access service resource | Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN). | gene ontology, human biology, genome, organism model, gene ontology consortium, FASEB list | NHGRI U41HG02223E | SCR_015850 | The Alliance | 2026-02-15 09:21:25 | 69 | ||||||||||
|
Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | software application, sequence analysis software, data processing software, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:barrnap, OMICS_13988 | https://github.com/tseemann/barrnap https://bio.tools/barrnap https://sources.debian.org/src/barrnap/ |
SCR_015995 | Barrnap: Basic rapid ribosomal RNA predictor | 2026-02-15 09:21:28 | 568 | |||||||
|
Aegean Resource Report Resource Website 1+ mentions |
Aegean (RRID:SCR_015965) | software application, sequence analysis software, data processing software, software resource, software toolkit, data analysis software | Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more. | genome, evaluation, annotation, structure, loci |
is listed by: Debian is listed by: OMICtools |
National Science Foundation 1126267 | PMID:22852583 | Free, Available for download, Freely available, | OMICS_19721 | https://github.com/BrendelGroup/AEGeAn https://sources.debian.org/src/aegean/ |
SCR_015965 | AEGeAn: analysis and evaluation of genome annotations, Aegean Toolkit | 2026-02-15 09:21:43 | 6 | |||||
|
andi Resource Report Resource Website 10+ mentions |
andi (RRID:SCR_015971) | software application, data processing software, algorithm resource, software resource, alignment software, image analysis software | Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes. | algorithm, computing, estimate, analysis, genome, alignment, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Deutsche Forschungsgemeinschaft Pf672/3-1 | PMID:25504847 | Free, Freely available, Available for download | OMICS_09287, biotools:andi | https://bio.tools/andi https://sources.debian.org/src/andi/ |
SCR_015971 | 2026-02-15 09:21:29 | 41 | ||||||
|
Cross-species scaffolding Resource Report Resource Website 1+ mentions |
Cross-species scaffolding (RRID:SCR_015932) | software application, sequence analysis software, source code, data processing software, software resource, data analysis software | Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references. | mate, pair, end, reference, genome | Free, Available for download, Freely available | SCR_016125 | SCR_015932 | cross-species-scaffolding | 2026-02-15 09:21:42 | 1 | |||||||||
|
Piggy Resource Report Resource Website 10+ mentions |
Piggy (RRID:SCR_015941) | software application, data processing software, data analysis software, software resource | Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary). | intergenic, region, bacterial, analysis, gene, genome, assembly | Medical Research Council | Free, Available for download | SCR_015941 | 2026-02-15 09:21:29 | 31 | ||||||||||
|
MetaNetX Resource Report Resource Website 50+ mentions |
MetaNetX (RRID:SCR_015882) | web service, data access protocol, software resource | Web application to perform automated model construction and genome annotation for large-scale metabolic networks. Platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways. | automated model construction, genome annotation, model, construction, genome, annotation, metabolic network, repository, gsm, biochemical, pathway | Swiss National Science Foundation ; Swiss Federal Government ; SIB Swiss Institute of Bioinformatics |
PMID:26527720 PMID:23357920 PMID:23172809 |
Free, Freely available | SCR_015882 | MNXref, MetaNetX: Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks | 2026-02-15 09:21:27 | 82 | ||||||||
|
EnrichmentMap Resource Report Resource Website 500+ mentions |
EnrichmentMap (RRID:SCR_016052) | software application, data visualization software, source code, data processing software, software resource | Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together. | cytoscape, functional, visualization, enrichment, gene, mapping, genome, pathway, network, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: Cytoscape |
NHGRI P41 HG04118; Ontario Genomics Institute ; Heart and Stroke Foundation of Canada ; Canada Foundation for Innovation ; Ontario Research Fund (ORF) |
PMID:21085593 | biotools:enrichmentmap | https://github.com/BaderLab/EnrichmentMapApp https://bio.tools/enrichmentmap |
SCR_016052 | 2026-02-15 09:21:31 | 545 | |||||||
|
Clonalframe Resource Report Resource Website 100+ mentions |
Clonalframe (RRID:SCR_016060) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. | analysis, sequence, inference, bacteria, microevolution, multilocus, clonal, sample, chromosome, homologuous, recombination, disrupted, inheritance, DNA, genome |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | DOI:10.1534/genetics.106.063305 | Free, Available for download | OMICS_14623 | https://github.com/xavierdidelot/ClonalFrameML https://sources.debian.org/src/clonalframe/ |
SCR_016060 | ClonalFrameML | 2026-02-15 09:21:31 | 379 | |||||
|
SwiftOrtho Resource Report Resource Website 1+ mentions |
SwiftOrtho (RRID:SCR_017122) | software application, data processing software, data analysis software, software resource | Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets. | orthology, analysis, identify, ortholog, paralog, co ortholog, genome, homology, different, species, large, dataset, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/543223 | Free, Available for download, Freely available | OMICS_30890, biotools:SwiftOrtho | https://bio.tools/SwiftOrtho | SCR_017122 | 2026-02-15 09:21:56 | 4 | |||||||
|
dndSCV Resource Report Resource Website 10+ mentions |
dndSCV (RRID:SCR_017093) | software application, data processing software, data analysis software, software resource | Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets. | dN/dS, method, quantify, selection, cancer, somatic, evolution, missense, nonsense, essential, splice, mutation, gene, genome, dataset |
uses: devtools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017093 | 2026-02-15 09:21:15 | 35 | ||||||||||
|
WTDBG Resource Report Resource Website 50+ mentions |
WTDBG (RRID:SCR_017225) | software application, sequence analysis software, data processing software, software resource, alignment software, image analysis software, data analysis software | Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time. | sequence, assembler, de novo, long, noisy, read, likelihood, estimator, genome |
is listed by: OMICtools is listed by: Debian |
NSFC ; NHGRI R01 HG010040 |
PMID:31819265 | Free, Available for download, Freely available | OMICS_24025 | https://github.com/ruanjue/wtdbg https://sources.debian.org/src/wtdbg2/ |
SCR_017225 | Wtdbg2, wtdgb, Wtdgb, wtdgb2 | 2026-02-15 09:22:00 | 57 | |||||
|
3D de novo assembly Resource Report Resource Website 10+ mentions |
3D de novo assembly (RRID:SCR_017227) | software application, data processing software, data analysis software, software resource | Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly. | de novo, assembly, 3D, DNA, HI-C, data, scaffold, pipeline, chromosome, genome | DOI:10.1126/science.aal3327 | Free, Available for download, Freely available | SCR_017227 | 2026-02-15 09:21:17 | 40 | ||||||||||
|
matemaker Resource Report Resource Website 1+ mentions |
matemaker (RRID:SCR_017199) | software application, sequence analysis software, data processing software, software resource, standalone software, data analysis software | Software tool to make artificial mate pairs from long sequences for scaffolding. | artificial, mate, pair, long, sequence, scaffolding, genomics, genome, assembly | Free, Available for download, Freely available | SCR_017199 | matemaker v1.0.0 | 2026-02-15 09:21:59 | 4 | ||||||||||
|
RNAmmer Resource Report Resource Website 100+ mentions |
RNAmmer (RRID:SCR_017075) | software application, data analysis service, data processing software, software resource, data access protocol, web service, service resource, standalone software, production service resource, analysis service resource, data analysis software | Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes. | predict, ribosomal, RNA, gene, full, genome, sequence, HMM, rRNA | has parent organization: Technical University of Denmark; Lyngby; Denmark | EMBIO at the University of Oslo ; Research Council of Norway ; Danish Center for Scientific Computing ; European Union |
PMID:17452365 | Restricted | SCR_017075 | 2026-02-15 09:21:14 | 103 |
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.
