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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | data visualization software, data processing software, data analysis software, software application, software resource | Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically. | data, mining, visualization, analysis, polychromatic, flow, cytometry, dataset, normalized, graphically, bio.tools |
is listed by: NIAID is listed by: Debian is listed by: bio.tools |
NIAID ; NIH |
PMID:21265010 | Free, Available for download, Freely available | biotools:spice | https://bio.tools/spice | SCR_016603 | Simplified Presentation of Incredibly Complex Evaluations | 2026-02-14 02:03:15 | 66 | ||||
|
Discovar assembler Resource Report Resource Website 10+ mentions |
Discovar assembler (RRID:SCR_016755) | Discovar | sequence analysis software, data processing software, data analysis software, software application, software resource | Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes. | variant, calling, reference, de novo, assembly, genome, genetic, human, sequence, analysis |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG003474; NHGRI U54 HG003067; NIAID HHSN272200900018C |
PMID:25326702 | Free, Available for download, Freely available | SCR_016755 | Discovar de novo, Discovar | 2026-02-14 02:03:05 | 20 | ||||||
|
SALSA Resource Report Resource Website 10+ mentions |
SALSA (RRID:SCR_022013) | data analysis software, software resource, data processing software, software application | Software tool for scaffold long read assemblies with Hi-C data. | scaffolding, Hi-C data, scaffold long read assemblies | NHGRI R44 HG009584; NIAID R01 AI100947; Ministry of Health and Welfare ; Republic of Korea |
DOI:10.1371/journal.pcbi.1007273 DOI:10.1186/s12864-017-3879-z |
Free, Available for download, Freely available | SCR_022013 | SALSA2 | 2026-02-14 02:04:24 | 40 | ||||||||
|
MCScanX Resource Report Resource Website 100+ mentions |
MCScanX (RRID:SCR_022067) | data processing software, data analysis software, software toolkit, software application, software resource | Software toolkit for detection and evolutionary analysis of gene synteny and collinearity. | gene synteny and collinearity, detection and evolutionary analysis, | NSF DBI 0849896; NSF MCB 0821096; NSF MCB 1021718; NIAID R01 AI068908 |
PMID:22217600 | Free, Available for download, Freely available | SCR_022067 | Multiple Collinearity Scan toolkit X version | 2026-02-14 02:04:25 | 257 | ||||||||
|
Stitchr Resource Report Resource Website 1+ mentions |
Stitchr (RRID:SCR_022139) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information. | Stitch together coding TCR nucleotide sequences, Python, T cell receptors nucleotide, V and J gene symbols, hypervariable CDR3 amino acid sequence, fully spliced TCR cDNA | NCI R01 CA164273; NIAID R43 AI120313; NCI R43 CA232942; Emily Venanzi Fund |
PMID:35325179 | Free, Available for download, Freely available | SCR_022139 | 2026-02-14 02:04:43 | 3 | |||||||||
|
Harmony Resource Report Resource Website 100+ mentions |
Harmony (RRID:SCR_022206) | data analysis software, software resource, data processing software, software application | Software R package to project cells into shared embedding in which cells group by cell type rather than dataset specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. Used for integration of single cell data. | cells grouping, cell type, experimental factors, biological factors, single cell data integration | is used by: harmonypy | NIAID U19 AI111224; NIH R01 AR063759; NIH UH2 AR067677; NIH T32 AR007530 |
PMID:31740819 | Free, Available for download, Freely available | SCR_022206 | Harmony for immunogenomics | 2026-02-14 02:04:27 | 171 | |||||||
|
ApiDots Resource Report Resource Website 1+ mentions |
ApiDots (RRID:SCR_001778) | data or information resource, database | Note: ApiDots is currently unavailable. For data on apicomplexan EST assemblies, please see EuPathDB ApiDots is a database integrating mRNA/EST sequences from numerous Apicomplexan parasites. ESTs and mRNAs were clustered and further assembled to generate consensus sequences. These consensus sequences were then subjected to database searches against protein sequences and protein domain sequences. The underlying relational structure of this database allows researchers to analyze these data and pose biologically interesting questions. | est, apicomplexan parasite, mrna, protein domain sequence, protein sequence |
is related to: Eukaryotic Pathogen Database Resources has parent organization: University of Pennsylvania; Philadelphia; USA |
USDA ; Amerman Family Foundation ; Merck Research Laboratories ; Burroughs Wellcome Fund ; NRI 99-35204-8615; NIAID AI45806; NIAID AI45806A1; NIAID AI48121 |
PMID:12618375 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02556 | SCR_001778 | 2026-02-14 02:05:36 | 2 | |||||||
|
HIV Molecular Immunology Database Resource Report Resource Website 1+ mentions |
HIV Molecular Immunology Database (RRID:SCR_002893) | HIV Molecular Immunology Database | data or information resource, database | An annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites, plus related tools and information. The goal of this database is to provide a comprehensive listing of defined HIV epitopes. These data are also printed in the HIV Molecular Immunology compendium, which is updated yearly and provided free of charge to scientific researchers, both by online download and as a printed copy. The data included in this database are extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL (CD8+), T helper (CD4+), and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, tables and maps of all defined linear epitopes relative to the HXB2 reference proteins are provided. Alignments of CTL, helper T-cell, and antibody epitopes are available through the search interfaces. Only responses to HIV-1 and HIV-2 are included in the database. | cytotoxic t cell, cytotoxic t lymphocyte, helper t-cell, antibody, binding site, epitope, t cell epitope, human immunodeficiency virus, immunology, molecule, genome, protein, alignment, b-cell, t-cell, annotation, ctl, t helper, coding region, cross-reactivity, escape mutation, antibody sequence, tcr usage, functional domain, immune response, progression, therapy | has parent organization: HIV Databases | Human immunodeficiency virus | NIAID | nif-0000-02965 | http://hiv-web.lanl.gov/immunology/ | SCR_002893 | Human Immunodeficiency Virus Molecular Immunology Database | 2026-02-14 02:05:41 | 2 | |||||
|
Nonhuman Primate HIV/SIV Vaccine Trials Database Resource Report Resource Website |
Nonhuman Primate HIV/SIV Vaccine Trials Database (RRID:SCR_002274) | data or information resource, database | An overview of HIV and SIV vaccine trials and their outcomes. It was developed as a tool for compilation, search and comparison of published studies on SIV, HIV and SHIV vaccine trials in nonhuman primates. We used a set of criteria to scan Pubmed for relevant studies to enter into the database. In selecting studies for entry, priority was given to recently published studies in journals generally regarded as the primary source of information pertaining to HIV and SIV vaccine research in nonhuman primates. In most cases, we give priority to challenge studies, where the animals received a live virus to measure the "efficacy" of the immunogen(s) inoculated during the course of the investigation. The HIV Sequence Database focuses on five primary goals: *Collecting HIV and SIV sequence data (all sequences since 1987) *Curating and annotating this data, and making it available to the scientific community *Computer analysis of HIV and related sequences *Production of software for the analysis of (sequence) data *Publication of the data and analyses on this site and in a yearly printed publication, the HIV sequence Compendium, which is available free of charge | drug, trial, vaccine, human immunodeficiency virus, simian immunodeficiency virus | has parent organization: HIV Databases | Human immunodeficiency virus, Simian immunodeficiency virus | NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20999 | http://hiv-web.lanl.gov/cgi-bin/vaccine/public/index.cgi | SCR_002274 | HIV/SIV Trials Vaccine DB, HIV/SIV Trials Vaccine Database | 2026-02-14 02:05:47 | 0 | |||||
|
Sparse Inverse Covariance Estimation for Ecological Association Inference Resource Report Resource Website 10+ mentions |
Sparse Inverse Covariance Estimation for Ecological Association Inference (RRID:SCR_022646) | SPIEC-EASI | software resource, software toolkit | Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets. | inverse covariance matrix estimation, sequencing data, microbial ecological networks inference, amplicon sequencing datasets microbial ecological networks, | NIAID T32AI007180; NIDDK R01 DK103358; NIGMS RO1 GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022646 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-02-14 02:07:36 | 12 | |||||||
|
SingleR Resource Report Resource Website 100+ mentions |
SingleR (RRID:SCR_023120) | software resource, software toolkit | Software R package for unbiased cell type recognition of scRNA-seq data. Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer cell of origin of each single cell independently. | unbiased cell type recognition, scRNA-seq data, reference transcriptomic datasets, pure cell types, infer cell of origin | UCSF Marcus Award ; NHLBI HL131560; UCSF Nina Ireland Program award ; NHLBI HL139897; NIAID |
PMID:30643263 | Free, Available for download, Freely available | https://github.com/dviraran/SingleR https://github.com/LTLA/SingleR |
SCR_023120 | Single-cell RNA-seq cell types Recognition | 2026-02-14 02:07:22 | 321 | |||||||
|
DADA2 Resource Report Resource Website 500+ mentions |
DADA2 (RRID:SCR_023519) | software resource, software toolkit | Open source software R package for modeling and correcting Illumina sequenced amplicon errors. Fast and accurate sample inference from amplicon data with single nucleotide resolution. | modeling and correcting amplicon errors, Illumina sequenced amplicon errors, amplicon errors, sample inference, amplicon data, single nucleotide resolution |
is used by: ImmuMicrobiome is related to: dadasnake has parent organization: Stanford University; Stanford; California |
NSF ; NIAID R01AI112401; Samarth Foundation |
PMID:27214047 | Free, Available for download, Freely available | https://bioconductor.org/packages/dada2/ | SCR_023519 | 2026-02-14 02:07:40 | 960 | |||||||
|
ATHLATES Resource Report Resource Website 1+ mentions |
ATHLATES (RRID:SCR_023689) | software resource, software toolkit | Software package for determining HLA genotypes for individuals from Illumina exome sequencing data. Program applies assembly, allele identification and allelic pair inference to short read sequences, and applies it to data from Illumina platforms. | Illumina, HLA genotypes determination, Illumina exome sequencing data, allele identification, allelic pair inference, short read sequence, | Washington University School of Medicine ; NIAID ; National Institutes of Health ; Department of Health and Human Services |
PMID:23748956 | Free, Available for download, Freely available | SCR_023689 | 2026-02-14 02:07:37 | 3 | |||||||||
|
ImmGen Resource Report Resource Website 100+ mentions |
ImmGen (RRID:SCR_021792) | data or information resource, database | Project combines immunology and computational biology laboratories in effort to establish complete road map of gene-expression and regulatory networks in all immune cells. Project will generate, with rigorously standardized conditions, complete compendium of genome-wide data sets showing expression of protein-coding genes for all defined cell populations of mouse immune system. | gene expression, regulatory networks, all immune cells, protein coding genes, mouse immune system | NIAID R24 AI072073 | PMID:18800157 PMID:32978299 |
Free, Freely available | SCR_021792 | Immunological Genome Project | 2026-02-14 02:06:56 | 258 | ||||||||
|
DICOMConvert Resource Report Resource Website |
DICOMConvert (RRID:SCR_014100) | software resource, standalone software, software application | A DICOM image converter based on the ITK IO mechanism for reading and writing images. The formats currently supported by the converter are DICOM to: Analyze (*.hdr); MetaImage (*.mhd); Nrrd (*.nhdr, *.nrrd). | standalone software, dicom, image converter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
Center for Infectious Disease Imaging ; NIAID ; NIBIB |
Available for download | SCR_014100 | Dicom Converter | 2026-02-14 02:07:19 | 0 | ||||||||
|
CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | data analytics software, software resource, software application | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
Doris Duke Charitable Foundation ; Damon Runyon Cancer Research Foundation ; B&J Cardan Oncology Research Fund ; Ludwig Institute for Cancer Research ; NCI U01 CA154969; NIAID U19 AI090019; NCI T32 CA09302; US Department of Defense ; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-02-14 02:07:28 | 1239 | ||||||
|
Tree-Based Pipeline Optimization Tool Resource Report Resource Website 1+ mentions |
Tree-Based Pipeline Optimization Tool (RRID:SCR_017531) | TPOT | software resource, software toolkit | Software Python package to automate building of ML pipelines by combining flexible expression tree representation of pipelines with stochastic search algorithms such as genetic programming. | Automated, machine, learning, optimize, pipeline, genetic, programming | NIAID R01 AI117694 | Free, Available for download, Freely available | SCR_017532 | https://epistasislab.github.io/tpot/ https://github.com/EpistasisLab/tpot |
SCR_017531 | Tree based Pipeline Optimization Tool | 2026-02-14 02:07:01 | 1 | ||||||
|
ApiDB CryptoDB Resource Report Resource Website 10+ mentions |
ApiDB CryptoDB (RRID:SCR_013455) | ApiDB CryptoDB | data or information resource, database | An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data | cryptosporidium parvum, cryptosporidium, cryptosporidium genome, cryptosporidium orf, cryptosporidium sage tag alignments, cryptosporidium snp, genomic sequence, dna motif, snp, est, orf, data set, bio.tools |
uses: SynView is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Eukaryotic Pathogen Database Resources |
NIAID contract HHSN266200400037C | PMID:16381902 | nif-0000-02698, biotools:cryptodb | https://bio.tools/cryptodb | http://cryptodb.org/ | SCR_013455 | CryptoDB, Cryptosporidium Genomics Resource | 2026-02-14 02:06:43 | 25 | ||||
|
Cytokine Registry Resource Report Resource Website 1+ mentions |
Cytokine Registry (RRID:SCR_014368) | data or information resource, database | A registry of cytokines, chemokines, and receptors generated for the purpose of collecting, integrating, and mapping between entity names and synonyms from several resources. These resources include MeSH, the Protein Ontology, EntrezGene, HGNC, MGI, UniProt and others. | cytokine, registry, innate immune system, chemokine, receptor |
uses: UniProt uses: MeSH uses: Plant Ontology uses: Mouse Genome Informatics (MGI) uses: HGNC uses: Entrez Gene is affiliated with: The Immunology Database and Analysis Portal (ImmPort) has parent organization: University of California at San Francisco; California; USA |
NIAID ; NIH ; Department of Health and Human Services |
Acknowledgement required, Registry file is available for download | SCR_014368 | ImmPort Cytokine Registry | 2026-02-14 02:06:27 | 1 | ||||||||
|
EPIMHC Resource Report Resource Website 1+ mentions |
EPIMHC (RRID:SCR_016279) | data or information resource, database | Database of naturally processed MHC-restricted peptide ligands and epitopes for customized computational vaccinology. | mhc, peptide, ligand, eiptope, vaccine, vaccinology, virology, t cell, immunogenic, molecule, virus | NIAID AI50900; NIAID AI43649; Molecular Immunology Foundation |
PMID:15657103 | Freely available, The research community can contribute to this resource | SCR_016279 | EPIMHC Database | 2026-02-14 02:06:30 | 4 |
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.
