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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BiGGR Resource Report Resource Website |
BiGGR (RRID:SCR_002854) | software resource | Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs. | standalone software, mac os x, unix/linux, windows, r, metabolomics, network, visualization, metabolic reconstruction, model |
uses: BiGG Database is listed by: OMICtools has parent organization: Bioconductor |
PMID:25806817 | Free, Freely available, Available for download | OMICS_02655 | SCR_002854 | BiGGR - Constraint based modeling in R using metabolic reconstruction databases | 2026-02-14 02:00:33 | 0 | |||||||
|
PAPi Resource Report Resource Website 50+ mentions |
PAPi (RRID:SCR_002857) | software resource | An R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20929912 | Free, Freely available, Available for download | OMICS_02653 | SCR_002857 | PAPi - Predict metabolic pathway activity based on metabolomics data, Pathway Activity Profiling | 2026-02-14 02:00:20 | 53 | |||||||
|
ArrayExpress Resource Report Resource Website 5000+ mentions |
ArrayExpress (RRID:SCR_002964) | ArrayExpress | data repository, storage service resource, catalog, data or information resource, service resource, database | International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus. | gold, standard, functional, genomics, data, collection, microarray, next, generation, sequencing, NGS, repository |
uses: MIAME uses: MINSEQE uses: Gene Expression Omnibus is used by: NIF Data Federation is used by: BioSample Database at EBI is used by: Integrated Datasets is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: OMICtools is listed by: re3data.org is related to: DDBJ Omics Archive is related to: MIAME is related to: Gene Expression Atlas is related to: Experimental Factor Ontology is related to: Bgee: dataBase for Gene Expression Evolution is related to: ISA Infrastructure for Managing Experimental Metadata is related to: FlyMine is related to: MAGE-TAB is related to: Experimental Factor Ontology is related to: Magic is related to: ArrayExpress (R) is related to: CancerMIRNome has parent organization: European Bioinformatics Institute |
European Union ; SLING 226073; European Commission ; Gen2Phen 200754; NHGRI P41 HG003619 |
PMID:23193272 PMID:21071405 |
Available Public or Private, Free, Available for download, The community can contribute to this resource, Acknowledgement requested, to access private data registration required | OMICS_01023, nif-0000-30123, r3d100010222 | http://www.ebi.ac.uk/microarray-as/ae https://doi.org/10.17616/R3302G |
SCR_002964 | , ArrayExpress, ArrayExpress - functional genomics data, ArrayExpress Archive | 2026-02-14 02:00:28 | 7529 | ||||
|
CNVassoc Resource Report Resource Website 1+ mentions |
CNVassoc (RRID:SCR_002901) | software resource | Software package that carries out association analysis of common copy number variants in population-based studies. It includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21609482 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02609 | SCR_002901 | CNVassoc: Association analysis of CNV data | 2026-02-14 02:00:27 | 1 | |||||||
|
SURPI Resource Report Resource Website 10+ mentions |
SURPI (RRID:SCR_003071) | SURPI | software resource | Software providing a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples. | pipeline, cloud based pipeline, pathogen identification |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
PMID:24899342 | OMICS_04623 | https://github.com/chiulab/surpi | SCR_003071 | Sequence-based Ultra-Rapid Pathogen Identification | 2026-02-14 02:00:38 | 13 | ||||||
|
MethDB Resource Report Resource Website 10+ mentions |
MethDB (RRID:SCR_003108) | MethDB | data repository, storage service resource, data or information resource, service resource, database | Database that provides a resource to store DNA methylation data and to make these data readily available to the public. Future development of the database will focus on environmental effects on DNA methylation. No restriction applies on the type of data, i.e. as well as global estimations (e.g. HPLC) as data from high resolution analysis (i.e. sequencing) can be stored. As much background information as possible should be provided by the users. This includes the origin of the sample, phenotype, expression of the related gene, etc.. | methylation |
is listed by: OMICtools has parent organization: University of Perpignan Via Domitia; Perpignan; France has parent organization: French National Center for Scientific Research |
PMID:11125109 PMID:17965614 PMID:12163707 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03119, OMICS_01840 | http://www.methdb.net/ | SCR_003108 | DNA Methylation Database, MethDB - the database for DNA methylation and environmental epigenetic effects | 2026-02-14 02:00:22 | 15 | |||||
|
FAS-DPD Resource Report Resource Website |
FAS-DPD (RRID:SCR_003068) | FAS-DPD | software resource | Software program to design degenerate primers for PCR. | command-line, java, primer, pcr, degenerate primer |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533783 | Free, Available for download, Freely available | OMICS_02340 | SCR_003068 | family-specific degenerate primer design | 2026-02-14 02:00:38 | 0 | ||||||
|
DnaSP Resource Report Resource Website 5000+ mentions |
DnaSP (RRID:SCR_003067) | DnaSP | data analysis software, software resource, data processing software, software application | A software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguad (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form. | genetics, dna, population genetics, sequence, polymorphism, nucleotide polymorphism, dna sequence, population, noncoding, synonymous, nonsynonymous |
is listed by: OMICtools has parent organization: University of Barcelona; Barcelona; Spain |
Spanish Direccion General de Investigacion Cientifica y Technica PB91-0245; Spanish Direccion General de Investigacion Cientifica y Technica PB94-0923; Spanish Direccion General de Investigacion Cientifica y Technica PB97-0918; Spanish Direccion General de Investigacion Cientifica y Technica TXT98-1802; Spanish Direccion General de Investigacion Cientifica y Technica BMC2001-2906; Spanish Direccion General de Investigacion Cientifica y Technica BFU2004-02253; Spanish Direccion General de Investigacion Cientifica y Technica BFU2007-6292 |
PMID:19346325 PMID:19378153 PMID:14668244 PMID:10089204 PMID:9183537 PMID:8808578 |
Free, Available for download, Freely available | OMICS_01820, nif-0000-30461 | SCR_003067 | DNA Sequence Polymorphism | 2026-02-14 02:00:22 | 5935 | |||||
|
JuncBASE Resource Report Resource Website 10+ mentions |
JuncBASE (RRID:SCR_003103) | data analysis software, software resource, data processing software, software application | Software used to identify and classify alternative splicing events from RNA-Seq data. JuncBASE also uses read counts to quantify the relative expression of each isoform and identifies splice events that are significantly differentially expressed across two or more samples. | splicing event, splicing events, alternative splicing event, rna seq |
is listed by: OMICtools is hosted by: GitHub |
Free, Available for download, Freely available | OMICS_01335 | https://github.com/anbrooks/juncBASE | SCR_003103 | 2026-02-14 02:00:39 | 19 | ||||||||
|
pFind Resource Report Resource Website 100+ mentions |
pFind (RRID:SCR_003011) | software resource | A search engine system for automated peptide and protein identification from tandem mass spectra. | mass spectrometry, proteomics |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:17702057 | OMICS_02467 | SCR_003011 | 2026-02-14 02:00:21 | 118 | |||||||||
|
JETTA Resource Report Resource Website 1+ mentions |
JETTA (RRID:SCR_003091) | JETTA | data analysis software, software resource, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 6, 2017. Software to detect alternatively spliced exons between two conditions, for example, between two groups of treated and untreated patients in a typical clinical study. | exon, exon splicing |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
PMID:22433281 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01334 | SCR_003091 | 2026-02-14 02:00:39 | 3 | |||||||
|
Primer3Plus Resource Report Resource Website 1000+ mentions |
Primer3Plus (RRID:SCR_003081) | Primer3Plus | data analysis service, analysis service resource, production service resource, source code, service resource, software resource | A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. | primer, dna sequence, primer design, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Primer3 has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
Howard Hughes Medical Institute ; NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:17485472 | Free, Freely available | biotools:primer3plus, OMICS_02347 | https://bio.tools/primer3plus | SCR_003081 | Primer3Plus - pick primers from a DNA sequence | 2026-02-14 02:00:29 | 1673 | ||||
|
tweeDEseq Resource Report Resource Website 1+ mentions |
tweeDEseq (RRID:SCR_003038) | software resource | Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. | standalone software, unix/linux, mac os x, windows, c, r, rna-seq, differential expression, sequencing, statistical method, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23965047 | Free, Available for download, Freely available | OMICS_02406, biotools:tweedeseq | https://bio.tools/tweedeseq | SCR_003038 | tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions | 2026-02-14 02:00:29 | 4 | ||||||
|
R-pbh5 Resource Report Resource Website |
R-pbh5 (RRID:SCR_003026) | software resource, software library, software toolkit | Software library for accessing data in HDF5 files produced by Pacific Biosciences sequencing machines. The R package supports accessing data from: cmp.h5, bas.h5, pls.h5, and trc.h5. | software package, r | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_05139 | https://github.com/extemporaneousb/R-pbh5 | SCR_003026 | 2026-02-14 02:00:37 | 0 | ||||||||
|
Isopat Resource Report Resource Website |
Isopat (RRID:SCR_003025) | software resource | Software function that calculates the isotopic pattern (fine structures) for a given chemical formula. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_02409 | https://isopat.sourceforge.net/ | SCR_003025 | isopat: Calculation of isotopic pattern for a given molecular formula | 2026-02-14 02:00:21 | 0 | |||||||
|
BRAIN Resource Report Resource Website 10+ mentions |
BRAIN (RRID:SCR_003018) | software resource | Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23350948 | GNU General Public License, v2 | biotools:brain, OMICS_02410 | https://bio.tools/brain | SCR_003018 | Baffling Recursive Algorithm for Isotopic distributioN calculations, Baffling Recursive Algorithm for Isotope distributioN | 2026-02-14 02:00:21 | 44 | ||||||
|
SASqPCR Resource Report Resource Website 1+ mentions |
SASqPCR (RRID:SCR_003056) | software resource | All-in-one computer program for robust and rapid analysis of quantitative reverse transcription real-time polymerase chain reaction (RT-qPCR) data in SAS. It incorporates all functions important for RT-qPCR data analysis including assessment of PCR efficiencies, validation of internal reference genes and normalizers, normalization of confounding variations across samples and statistical comparisons of target gene expression in parallel samples. The program is highly automatic in data analyses and result output. The input data have no limitations for the number of genes or cDNA samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. The program is also extendable allowing advanced SAS users to develop particular statistical tests appropriate for their experimental designs. Thus users are the actual decision-makers controlling RT-qPCR data analyses. The program has to be used in SAS software; however, extensive SAS programming knowledge is not required. | standalone software, computation, analysis, statistics, rt-qpcr, cdna, mrna, gene expression, quantification, reference gene, normalization, sas |
is listed by: OMICtools has parent organization: Google Code |
PMID:22238653 | Free, Available for download, Freely available | OMICS_02375 | SCR_003056 | SASqPCR: robust and rapid analysis of RT-qPCR data in SAS | 2026-02-14 02:00:38 | 6 | |||||||
|
SurvComp Resource Report Resource Website 50+ mentions |
SurvComp (RRID:SCR_003054) | survcomp | software resource | R package providing functions to assess and to compare the performance of risk prediction (survival) models. | differential expression, gene expression, visualization, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21903630 | Free, Available for download, Freely available | OMICS_02373 | SCR_003054 | survcomp - Performance Assessment and Comparison for Survival Analysis | 2026-02-14 02:00:38 | 58 | ||||||
|
Parametric Time Warping Resource Report Resource Website |
Parametric Time Warping (RRID:SCR_003053) | ptw | software resource | Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:14719890 | Free, Freely available | OMICS_02392 | SCR_003053 | ptw: Parametric Time Warping | 2026-02-14 02:00:29 | 0 | ||||||
|
Gutentag Resource Report Resource Website |
Gutentag (RRID:SCR_003051) | software resource | An interactive, user-editable genetic sequence database tool, targeted at molecular biology research groups that can be browsed using tags. The tool is Web 2.0-flavoured, allowing users to do more than just retrieve information. Its focus on user-editability is supported by the use of tags (metadata) associated with genetic sequences. Several methods of retrieving stored data are available including tag-clouds, BLAST and keyword searches. Also, sequence tags related to HGNC gene names, conserved domains (CDD) and GO terms can be automatically generated given sequence data. The tool is constructed using the high-level Python web framework, Django, with a SQLite3 backend. | standalone software, python, django, genetics, sequence |
is listed by: OMICtools has parent organization: Google Code |
PMID:14640709 | Free, Available for download, Freely available | OMICS_02396 | SCR_003051 | gutentag - A genetic sequence database for labs that can be browsed using tags | 2026-02-14 02:00:21 | 0 |
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.
