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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
HLASeq Resource Report Resource Website |
HLASeq (RRID:SCR_004185) | HLASeq | software resource | An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data. | genotyping, hla, next generation sequencing, gene, command-line, python |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01543 | SCR_004185 | SciCrunch Registry | 2026-11-07 11:55:45 | 0 | ||||||||
|
PASS-bis Resource Report Resource Website |
PASS-bis (RRID:SCR_004176) | PASS-bis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads. |
is listed by: OMICtools is related to: PASS |
PMID:23162053 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00587 | SCR_004176 | SciCrunch Registry | 2026-11-07 11:55:23 | 0 | ||||||||
|
BSRD Resource Report Resource Website 10+ mentions |
BSRD (RRID:SCR_004249) | BSRD | data or information resource, data repository, database, service resource, storage service resource | A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets. | srna target, srna, small regulatory non-coding rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23203879 | Acknowledgement requested, The community can contribute to this resource | biotools:bsrd, OMICS_01533 | https://bio.tools/bsrd | SCR_004249 | SciCrunch Registry | BSRD - Bacterial Small Regulatory RNA Database, Bacterial Small Regulatory RNA Database | 2026-11-07 11:55:18 | 29 | |||||
|
CDP Resource Report Resource Website 10+ mentions |
CDP (RRID:SCR_004236) | CDP | data or information resource, funding resource, portal, topical portal | National program to improve the diagnosis and assessment of cancer by moving scientific knowledge into clinical practice by coordinating and funding resources and research for the development of innovative in vitro diagnostics, novel diagnostic technologies and appropriate human specimens. The Cancer Diagnosis Program is divided into four branches: Biorepository and Biospecimen Research Branch (BBRB), Diagnostic Biomarkers and Technology Branch (DBTB), Diagnostics Evaluation Branch (DEB), and the Pathology Investigation and Resources Branch (PIRB). | cancer research, cancer funding, cancer research funding |
is listed by: OMICtools has parent organization: DCTD |
Cancer | NCI | Available to cancer researchers | OMICS_01536 | SCR_004236 | SciCrunch Registry | Cancer Diagnosis Program | 2026-11-07 11:55:18 | 19 | |||||
|
DRUT Resource Report Resource Website |
DRUT (RRID:SCR_004351) | DRUT | software resource | Software for Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data. | c++, reconstruction, frequency estimation, transcript, rna-seq, annotation |
is listed by: OMICtools has parent organization: Georgia State University; Georgia; USA |
NSF IIS-0546457; NSF IIS-0916401; NSF IIS-0916948 |
PMID:23202426 | OMICS_01273 | SCR_004351 | SciCrunch Registry | Discovery and Reconstruction of Unannotated Transcripts | 2026-11-07 11:55:13 | 0 | ||||||
|
Taverna Resource Report Resource Website 10+ mentions |
Taverna (RRID:SCR_004437) | Taverna | data processing software, software application, software resource, workflow software | An open source and domain independent Workflow Management System ����?? a suite of tools used to design and execute scientific workflows and aid in silico experimentation. Taverna Workbench now has support for service sets, offline workflow editing, workflow validation, improved workflow run monitoring, and the pausing and canceling of workflow runs. The command line tool allows you to run workflows outside of the workbench and is available as a stand-alone download or bundled with the Taverna Workbench 2.2.0 download. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick execution of workflows from a terminal. Taverna 2.2.0 includes * Copy/paste, shortcuts, undo/redo, drag and drop * Animated workflow diagram * Remembers added/removed services * Secure Web services support * Secure access to resources on the web * Up-to-date R support * Intermediate values during workflow runs * myExperiment integration * Excel and csv spreadsheet support * Command line tool |
is listed by: OMICtools is listed by: SoftCite is related to: myExperiment is related to: U-Compare is related to: Taverna Knowledge Blog is related to: AIDA Toolkit is related to: Knowledge Blog has parent organization: University of Manchester; Manchester; United Kingdom |
OMII-UK ; EPSRC ; BBSRC ; Microsoft ; ESRC ; JISC |
PMID:18337261 PMID:23640334 |
Open unspecified license | nlx_43462, OMICS_01146 | SCR_004437 | SciCrunch Registry | 2026-11-07 11:55:14 | 30 | |||||||
|
STAR Resource Report Resource Website 10000+ mentions |
STAR (RRID:SCR_004463) | alignment software, data processing software, image analysis software, software application, software resource | Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays. | RNA-seq data, alignment, RNA-seq reads alignment, reference genome, using uncompressed suffix arrays, bio.tools |
is used by: STARsolo is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U54 HG004557 | PMID:23104886 DOI:10.1093/bioinformatics/bts635 |
biotools:star, OMICS_01254, SCR_015899 | https://github.com/alexdobin/STAR, https://bio.tools/star, https://sources.debian.org/src/rna-star/ | SCR_004463 | SciCrunch Registry | Spliced Transcripts Alignment to Reference, Spliced Transcripts Alignment to a Reference (STAR), rna-star, ultrafast universal RNA-seq aligner | 2026-11-07 11:55:21 | 26381 | ||||||
|
ACT: Artemis Comparison Tool Resource Report Resource Website 10+ mentions |
ACT: Artemis Comparison Tool (RRID:SCR_004507) | ACT | software resource | A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | dna sequence, genome, synteny, pairwise comparison |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | PMID:15976072 | GNU General Public License | OMICS_00928, nlx_48986 | SCR_004507 | SciCrunch Registry | Artemis Comparison Tool | 2026-11-07 11:55:22 | 47 | |||||
|
Squeezambler Resource Report Resource Website |
Squeezambler (RRID:SCR_004385) | Squeezambler | software resource | Software to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather than the number of cells. |
is listed by: OMICtools has parent organization: Wayne State University; Michigan; USA |
PMID:23918251 | OMICS_01503 | SCR_004385 | SciCrunch Registry | 2026-11-07 11:55:27 | 0 | |||||||||
|
SNiPer-HD Resource Report Resource Website 1+ mentions |
SNiPer-HD (RRID:SCR_004383) | SNiPer-HD | software resource | Improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. | is listed by: OMICtools | PMID:17062589 | OMICS_00735 | SCR_004383 | SciCrunch Registry | SNiPer-HD: Improved genotype calling accuracy | 2026-11-07 11:55:13 | 2 | ||||||||
|
Vanator Resource Report Resource Website 1+ mentions |
Vanator (RRID:SCR_004370) | Vanator | software resource | A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples. | perl, metagenomic, illumina, alignment, assembly, analysis, profile, virus, clinical, environment, next-generation sequencing, taxonomy, read |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Glasgow; Glasgow; United Kingdom |
PMID:23296970 | OMICS_01505 | SCR_004370 | SciCrunch Registry | Vanator-CVR, Vanator-CVR - A metagenomics & virus discovery pipeline, Virus Alignment de Novo Assembly and Taxonomy On Reads, Vanator-CVR: A metagenomics and virus discovery pipeline | 2026-11-07 11:55:13 | 2 | |||||||
|
Basic OligoNucleotide Design Resource Report Resource Website 10+ mentions |
Basic OligoNucleotide Design (RRID:SCR_004492) | BOND | software resource | Software program to compute highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs. | dna, oligonucleotide, design, oligonucleotide design |
is listed by: OMICtools has parent organization: Western University; Ontario; Canada |
PMID:23444904 | OMICS_00827 | SCR_004492 | SciCrunch Registry | BOND: Basic OligoNucleotide Design | 2026-11-07 11:55:30 | 18 | |||||||
|
SOrt-ITEMS Resource Report Resource Website 1+ mentions |
SOrt-ITEMS (RRID:SCR_004716) | SOrt-ITEMS | software resource | Sequence orthology based software for improved taxonomic estimation of metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | metagenome, taxonomy, sequence, orthology, binning | is listed by: OMICtools | PMID:19439565 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01465 | SCR_004716 | SciCrunch Registry | Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences, SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences | 2026-11-07 11:55:24 | 6 | ||||||
|
UnifiedGenotyper Resource Report Resource Website 500+ mentions |
UnifiedGenotyper (RRID:SCR_004710) | UnifiedGenotyper | software resource | A multiple-sample, technology-aware SNP and indel caller. |
is listed by: OMICtools has parent organization: Broad Institute |
OMICS_00080 | SCR_004710 | SciCrunch Registry | 2026-11-07 11:55:35 | 562 | ||||||||||
|
NuChart Resource Report Resource Website 1+ mentions |
NuChart (RRID:SCR_004703) | NuChart | software resource | An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations. | is listed by: OMICtools | OMICS_00525 | SCR_004703 | SciCrunch Registry | 2026-11-07 11:55:49 | 2 | ||||||||||
|
Pplacer Resource Report Resource Website 10+ mentions |
Pplacer (RRID:SCR_004737) | Pplacer | software resource | Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. | classification, phylogenetic classification |
is listed by: OMICtools has parent organization: Fred Hutchinson Cancer Center |
PMID:21034504 | OMICS_01462 | SCR_004737 | SciCrunch Registry | pplacer: phylogenetic placement and downstream analysis | 2026-11-07 11:55:49 | 30 | |||||||
|
TETRA Resource Report Resource Website 50+ mentions |
TETRA (RRID:SCR_004573) | TETRA | software resource | Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences. | tetranucleotide, dna sequence |
is listed by: OMICtools has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany |
PMID:15305919 PMID:15507136 |
OMICS_01474 | SCR_004573 | SciCrunch Registry | TETRA - Fragment assignment by intrinsic tetranucleotide frequencies | 2026-11-07 11:55:48 | 68 | |||||||
|
QuickGO Resource Report Resource Website 500+ mentions |
QuickGO (RRID:SCR_004608) | QuickGO | controlled vocabulary, data access protocol, data or information resource, database, ontology, software resource, web service | A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services. | gene, ontology, annotation, browser, visualization, search engine, slimmer-type tool, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, windows, mac os x, linux, unix, gold standard, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: STRAP has parent organization: European Bioinformatics Institute |
BBSRC BB/E023541/1 | PMID:19744993 PMID:20157483 |
Apache License, v2, Free for academic use | biotools:quickgo, nlx_60318, OMICS_02276 | https://bio.tools/quickgo | SCR_004608 | SciCrunch Registry | Quick GO | 2026-11-07 11:55:23 | 556 | ||||
|
BioPig Resource Report Resource Website 1+ mentions |
BioPig (RRID:SCR_004636) | BioPig | software resource | Software providing a framework for genomic data analysis using Apache Pig and Hadoop. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
PMID:24021384 | biotools:biopig, OMICS_01225 | https://bio.tools/biopig | SCR_004636 | SciCrunch Registry | 2026-11-07 11:55:33 | 2 | |||||||
|
Nonpareil Resource Report Resource Website 50+ mentions |
Nonpareil (RRID:SCR_004629) | Nonpareil | software resource | Estimate average coverage and create Nonpareil curves for metagenomic datasets. | is listed by: OMICtools | PMID:24123672 | OMICS_01419 | SCR_004629 | SciCrunch Registry | 2026-11-07 11:55:48 | 96 |
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.
