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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GENERECON Resource Report Resource Website 1+ mentions |
GENERECON (RRID:SCR_009195) | GENERECON | software resource, software application | Software application for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, linux, macos, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154338, biotools:generecon | https://bio.tools/generecon | SCR_009195 | 2026-08-07 09:26:59 | 1 | ||||||||
|
HTR Resource Report Resource Website 1+ mentions |
HTR (RRID:SCR_009241) | HTR | software resource, software application | Software application for haplotype association mapping using unrelated individuals; fixed and sliding window analysis; overall tests and tests for individual haplotype effects (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, bash shell, ms-windows, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154402, biotools:htr | https://bio.tools/htr | SCR_009241 | Haplotype Trend Regression | 2026-08-07 09:27:00 | 1 | |||||||
|
rSeq Resource Report Resource Website 1+ mentions |
rSeq (RRID:SCR_000562) | software resource, software toolkit, source code | A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations. | rna, sequence, read quality assessment, reference sequence generation, sequence mapping, gene, isoform expressions estimations, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
Free, Available for download, Freely available, | OMICS_01288, biotools:rseq | https://bio.tools/rseq | SCR_000562 | RNA-Seq Analyzer, rSeq: RNA-Seq Analyzer | 2026-08-07 09:25:02 | 4 | |||||||
|
CODEHOP Resource Report Resource Website 50+ mentions |
CODEHOP (RRID:SCR_002898) | CODEHOP | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Service to design PCR primers from protein multiple sequence alignments. NOTICE: This version of CODEHOP is no longer maintained. | degenerate, primer, primer design, degenerate primer, oligonucleotide, pcr assay, gene, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Fred Hutchinson Cancer Center |
PMID:20967601 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:codehop, OMICS_02339 | https://bio.tools/codehop | SCR_002898 | COnsensus-DEgenerate Hybrid Oligonucleotide Primers, CODEHOP: COnsensus-DEgenerate Hybrid Oligonucleotide Primers | 2026-08-07 09:25:32 | 75 | |||||
|
DictyOGlyc Resource Report Resource Website 10+ mentions |
DictyOGlyc (RRID:SCR_001600) | DictyOGlyc | analysis service resource, data analysis service, production service resource, service resource | Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins. | glcnac glycosylation site, neural network, o-glycosylation, prediction, proteome, glycoprotein, glcnac, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: CBS Prediction Servers |
Deutscher Akademischer Austauschdienst ; HspII/AUFE ; Macquarie University International Postgraduate Research Award ; Australian Research Council ; National Health and MRC ; Danish National Research Foundation |
PMID:10521537 | Free, Freely available | nlx_153856, biotools:dictyoglyc | https://bio.tools/dictyoglyc | SCR_001600 | 2026-08-07 09:25:14 | 17 | |||||
|
GlyProt Resource Report Resource Website 10+ mentions |
GlyProt (RRID:SCR_001560) | GlyProt | analysis service resource, data analysis service, production service resource, service resource | Web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II, http://www.glycosciences.de/modeling/sweet2/doc/index.php | glycosylation, protein, in silico, 3d structure, protein structure, glycan, n-glycan, glycoprotein, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: SWEET-DB has parent organization: glycosciences.de |
DFG | PMID:15980456 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:glyprot, nlx_152875 | https://bio.tools/glyprot | http://www.glycosciences.de/glyprot/ | SCR_001560 | GlyProt - In Silico Glycosylation of Proteins | 2026-08-07 09:25:14 | 39 | |||
|
HiPipe Resource Report Resource Website 1+ mentions |
HiPipe (RRID:SCR_001215) | HiPipe | analysis service resource, data analysis service, production service resource, service resource | Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task. | next-generation sequencing, dna, rna, differential expression, mirna, gene fusion, variant, genome, exome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Academia Sinica; Taipei; Taiwan |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02128, biotools:hipipe | https://bio.tools/hipipe | SCR_001215 | HiPipe - High Performance Pipelines for NGS Data Analysis | 2026-08-07 09:25:10 | 2 | ||||||
|
GeneFisher Resource Report Resource Website 10+ mentions |
GeneFisher (RRID:SCR_003060) | GeneFisher, GeneFisher2 | analysis service resource, data analysis service, production service resource, service resource | A web-based program for designing degenerate primers. The procedure leads to isolation of genes in a target organism using multiple alignments of related genes from different organisms. The term gene fishing refers to the technique where PCR is used to isolate a postulated but unknown target sequence from a pool of DNA. | primer design, gene, degenerate primer, degenerate, primer, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:8877506 | Free, Freely available | biotools:genefisher, OMICS_02341 | https://bio.tools/genefisher | SCR_003060 | GeneFisher2 - Interactive PCR Primer Design | 2026-08-07 09:25:34 | 39 | |||||
|
ResponseNet Resource Report Resource Website 1+ mentions |
ResponseNet (RRID:SCR_003176) | ResponseNet | analysis service resource, data analysis service, production service resource, service resource | WebServer that identifies high-probability signaling and regulatory paths that connect input data sets. The input includes two weighted lists of condition-related proteins and genes, such as a set of disease-associated proteins and a set of differentially expressed disease genes, and a molecular interaction network (i.e., interactome). The output is a sparse, high-probability interactome sub-network connecting the two sets that is biased toward signaling pathways. This sub-network exposes additional proteins that are potentially involved in the studied condition and their likely modes of action. Computationally, it is formulated as a minimum-cost flow optimization problem that is solved using linear programming. | interactome, gene, protein, signaling pathway, signaling, regulatory, pathway, regulatory pathway, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel |
PMID:23761447 PMID:21576238 |
Free, Freely available | biotools:responsenet, OMICS_01562 | https://bio.tools/responsenet | http://netbio.bgu.ac.il/respnet/ | SCR_003176 | 2026-08-07 09:25:36 | 4 | |||||
|
Information Hyperlinked Over Proteins Resource Report Resource Website 10+ mentions |
Information Hyperlinked Over Proteins (RRID:SCR_004829) | iHOP | database, data or information resource, service resource | Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli. | phenotype, gene, protein, interaction, pathology, physiology, gene network, network, literature, gene function, text-mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PubMed has parent organization: Autonomous University of Madrid; Madrid; Spain |
European Union IST-2001- 32688; European Union QLRT-2001-00015 |
PMID:15226743 | Creative Commons Attribution-NoDerivs License, Works v3 | biotools:ihop, nif-0000-00232, OMICS_01185 | https://bio.tools/ihop | SCR_004829 | iHOP - Information Hyperlinked over Proteins | 2026-08-07 09:26:02 | 24 | ||||
|
PILGRM Resource Report Resource Website 1+ mentions |
PILGRM (RRID:SCR_004749) | PILGRIM | analysis service resource, data analysis service, production service resource, service resource | PILGRM (the platform for interactive learning by genomics results mining) puts advanced supervised analysis techniques applied to enormous gene expression compendia into the hands of bench biologists. This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner. This capability allows domain experts to quickly and easily generate hypotheses about biological processes, tissues or diseases of interest. Specifically PILGRM helps biologists generate these hypotheses by analyzing the expression levels of known relevant genes in large compendia of microarray data. PILGRM is for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). PILGRM produces publication quality PDFs usable as supplementary material to describe the computational approach, standards and datasets. Each PILGRM analysis starts with an important biological question (e.g. What genes are relevant for breast cancer but not mammary tissue in general?). For PILGRM to discover relevant genes, it needs examples of both genes that you would (positive) and would not (negative) find interesting. Lists of these genes are what we call standards and in PILGRM you can build your own standards or you can use standards from common sources that we pre-load for your convenience. PILGRM lets you build your own literature-documented standards so that processes, disease, and tissues that are not well covered in databases of tissue expression, disease, or function can still be used for an analysis. | data mining, gene expression, user directed data mining, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Princeton University; New Jersey; USA |
NSF DBI-0546275; NIGMS R01 GM071966; NIGMS P50 GM071508; NCI T32 CA005928 |
PMID:21653547 | nlx_75372, biotools:pilgrm | https://bio.tools/pilgrm | SCR_004749 | Platform for Interactive Learning by Genomics Results Mining | 2026-08-07 09:26:01 | 1 | |||||
|
MG-RAST Resource Report Resource Website 1000+ mentions |
MG-RAST (RRID:SCR_004814) | MG RAST | analysis service resource, data analysis service, production service resource, service resource | An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples. | metagenome, base pair, sequence, phylogenetic, functional analysis, data sharing, metadata, protein, micro biome, analysis platform, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: Argonne National Laboratory |
NIAID contract HHSN272200900040C; DOE contract DE-AC02-06CH11357 |
PMID:18803844 | Acknowledgement requested, Public, Account required | OMICS_01456, biotools:mg-rast | http://metagenomics.nmpdr.org, https://bio.tools/mg-rast | SCR_004814 | The Metagenomics RAST server, Metagenomics RAST, MG-RAST - metagenomics analysis server | 2026-08-07 09:25:59 | 1165 | ||||
|
StSNP Resource Report Resource Website 1+ mentions |
StSNP (RRID:SCR_005417) | StSNP | analysis service resource, data analysis service, production service resource, service resource | A web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00138, biotools:stsnp | https://bio.tools/stsnp | SCR_005417 | Structure SNP | 2026-08-07 09:26:07 | 3 | |||||||
|
PRINSEQ Resource Report Resource Website 1000+ mentions |
PRINSEQ (RRID:SCR_005454) | PRINSEQ | analysis service resource, data analysis service, production service resource, service resource | A publicly available tool that is able to filter, reformat and trim your genomic and metagenomic sequence data and provide you summary statistics for your sequence data. The interactive web interface facilitates visualizations of the results and export functionality for subsequent data processing. The standalone lite version is written in Perl and does not require any non-core Perl modules. The lite version is primarily designed for data preprocessing and does not generate summary statistics in graphical form., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, data analysis, genomic sequence data, metagenomic sequence data, summary, perl, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: San Diego State University; California; USA |
PMID:21278185 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01068, biotools:prinseq | http://prinseq.sourceforge.net, https://bio.tools/prinseq | SCR_005454 | PReprocessing and INformation of SEQuences, preprocessing and information of sequences | 2026-08-07 09:26:12 | 1199 | |||||
|
TMA Navigator Resource Report Resource Website 1+ mentions |
TMA Navigator (RRID:SCR_005599) | TMA Navigator | analysis service resource, data analysis service, production service resource, service resource | A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement. | tissue microarray, network, analysis, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23761446 | Acknowledgement requested, Free | biotools:tma_navigator, OMICS_00821 | https://bio.tools/tma_navigator | SCR_005599 | 2026-08-07 09:26:07 | 5 | ||||||
|
SPOT - Biological prioritization after a SNP association study Resource Report Resource Website 500+ mentions |
SPOT - Biological prioritization after a SNP association study (RRID:SCR_005193) | SPOT | analysis service resource, data analysis service, production service resource, service resource | A web-based tool for using biological databases to prioritize single nucleotide polymorphisms (SNPs) after a genome-wide association study (GWAS). The site allows users to upload a list of SNPs and GWAS P-values and returns a prioritized list of SNPs using the GIN method. Users can specify candidate genes or genomic regions with custom levels of prioritization. The results can be downloaded or viewed in the browser where users can interactively explore the details of each SNP, including graphical representations of the genomic information network (GIN) method. For investigators interested in incorporating biological databases into a post-GWAS SNP selection strategy, the SPOT web tool is an easily implemented and flexible solution. | single nucleotide polymorphism, genome-wide association study, linkage disequilibrium, gene, genomic region, p-value, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:20529875 | biotools:spot, OMICS_00189 | https://bio.tools/spot | SCR_005193 | 2026-08-07 09:26:09 | 512 | |||||||
|
GoMapMan Resource Report Resource Website 10+ mentions |
GoMapMan (RRID:SCR_005060) | GoMapMan | database, data or information resource, service resource | An open web-accessible resource for gene functional annotations in the plant sciences to facilitate improvement, consolidation and visualization of gene annotations across several plant species. It is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis, potato, tomato, rice, and tobacco are included. The main features are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes. | functional annotation, function, annotation, gene, visualization, ortholog, ontology, microarray, gene annotation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Set Enrichment Analysis is related to: MapMan is related to: Biomine is related to: SEGS has parent organization: Jozef Stefan Institute; Ljubljana; Slovenia |
Slovenian Research Agency J4-2228; Slovenian Research Agency P2-0103 |
PMID:24194592 | Creative Commons Attribution-NonCommercial-ShareAlike License | biotools:gomapman, OMICS_02280 | https://bio.tools/gomapman | SCR_005060 | 2026-08-07 09:26:02 | 29 | |||||
|
Human Splicing Finder Resource Report Resource Website 1000+ mentions |
Human Splicing Finder (RRID:SCR_005181) | HSF | analysis service resource, data analysis service, production service resource, service resource | Software tool to help study pre-mRNA splicing and to better understand intronic and exonic mutations leading to splicing defects. To calculate the consensus values of potential splice sites and search for branch points, new algorithms were developed. Furthermore, they have integrated all available matrices to identify exonic and intronic motifs, as well as new matrices to identify hnRNP A1, Tra2-? and 9G8. | splicing, mutation, splicing signal, sequence, transcript, nucleotide, exon, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Ensembl has parent organization: National Institute of Health and Medical Research; Rennes; France |
PMID:19339519 | Acknowledgement requested | biotools:human_splicing_finder, OMICS_00176 | https://bio.tools/human_splicing_finder | http://www.umd.be/HSF/ | SCR_005181 | 2026-08-07 09:26:04 | 1009 | |||||
|
ADGO Resource Report Resource Website 1+ mentions |
ADGO (RRID:SCR_006343) | ADGO | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. | microarray, gene, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21624890 | Acknowledgement requested | OMICS_02229, biotools:adgo | https://bio.tools/adgo | SCR_006343 | 2026-08-07 09:26:19 | 3 | ||||||
|
HMM-TM Resource Report Resource Website 1+ mentions |
HMM-TM (RRID:SCR_006186) | HMM-TM | analysis service resource, data analysis service, production service resource, service resource | A web tool using the Hidden Markov Model method for the topology prediction of alpha-helical membrane proteins that incorporates experimentally derived topological information. Hidden Markov Models (HMMs) have been extensively used in computational molecular biology, for modelling protein and nucleic acid sequences. In many applications, such as transmembrane protein topology prediction, the incorporation of limited amount of information regarding the topology, arising from biochemical experiments, has been proved a very useful strategy that increased remarkably the performance of even the top-scoring methods. However, no clear and formal explanation of the algorithms that retains the probabilistic interpretation of the models has been presented so far in the literature. We present here, a simple method that allows incorporation of prior topological information concerning the sequences at hand, while at the same time the HMMs retain their full probabilistic interpretation in terms of conditional probabilities. We present modifications to the standard Forward and Backward algorithms of HMMs and we also show explicitly, how reliable predictions may arise by these modifications, using all the algorithms currently available for decoding HMMs. A similar procedure may be used in the training procedure, aiming at optimizing the labels of the HMM''s classes, especially in cases such as transmembrane proteins where the labels of the membrane-spanning segments are inherently misplaced. We present an application of this approach developing a method to predict the transmembrane regions of alpha-helical membrane proteins, trained on crystallographically solved data. We show that this method compares well against already established algorithms presented in the literature, and it is extremely useful in practical applications. | hidden markov model, topology, prediction, alpha-helical membrane protein, protein, transmembrane, transmembrane alpha-helical protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:16597327 | Free for academic use | nlx_151731, biotools:hmm-tm | https://bio.tools/hmm-tm | SCR_006186 | HMM-TM: Prediction of Transmembrane Alpha-Helical Proteins | 2026-08-07 09:26:18 | 7 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
