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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Oases Resource Report Resource Website 100+ mentions |
Oases (RRID:SCR_011896) | Oases | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. | bio.tools, transcriptome assembler |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
DOI:10.1093/bioinformatics/bts094 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:oases, OMICS_01322 | https://bio.tools/oases | https://sources.debian.org/src/oases/ | SCR_011896 | 2026-02-07 02:08:18 | 289 | |||||
|
Rnnotator Resource Report Resource Website 10+ mentions |
Rnnotator (RRID:SCR_011897) | Rnnotator | software resource | Software designed to assemble Illumina single or paired-end reads. |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
OMICS_01323 | SCR_011897 | 2026-02-07 02:08:24 | 24 | ||||||||||
|
STM Resource Report Resource Website |
STM (RRID:SCR_011898) | STM | software resource | A de novo transcriptome assembly from next-generation sequencing data. | is listed by: OMICtools | OMICS_01325 | SCR_011898 | 2026-02-07 02:08:26 | 0 | ||||||||||
|
TopHat-Fusion Resource Report Resource Website 100+ mentions |
TopHat-Fusion (RRID:SCR_011899) | TopHat-Fusion | software resource | An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21835007 | OMICS_01359, biotools:tophat-fusion | https://bio.tools/tophat-fusion | SCR_011899 | TopHat-Fusion: An algorithm for Discovery of Novel Fusion Transcripts | 2026-02-07 02:08:18 | 156 | ||||||
|
Glimmer-MG Resource Report Resource Website 1+ mentions |
Glimmer-MG (RRID:SCR_011932) | Glimmer-MG | software resource | A software system for finding genes in environmental shotgun DNA sequences. | metagenomics, gene |
is listed by: OMICtools is related to: Glimmer has parent organization: University of Maryland; Maryland; USA |
Open unspecified license, OSI certified | OMICS_01487 | SCR_011932 | Glimmer-MG: Metagenomics Gene-Finding System, Gene Locator and Interpolated Markov ModelER - MetaGenomics | 2026-02-07 02:08:19 | 8 | |||||||
|
MetaGeneAnnotator Resource Report Resource Website 50+ mentions |
MetaGeneAnnotator (RRID:SCR_011934) | MetaGeneAnnotator | software resource | A gene-finding software program for prokaryote and phage., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01490 | SCR_011934 | 2026-02-07 02:08:27 | 88 | |||||||||
|
MGC Resource Report Resource Website |
MGC (RRID:SCR_011935) | MGC | software resource | A software application for finding complete and incomplete genes in metagenomic reads. |
is used by: EMBRYS is listed by: OMICtools |
OMICS_01491 | SCR_011935 | 2026-02-07 02:08:25 | 0 | ||||||||||
|
MetaSim Resource Report Resource Website 10+ mentions |
MetaSim (RRID:SCR_011940) | MetaSim | software resource | A Sequencing Simulator for Genomics and Metagenomics. | is listed by: OMICtools | OMICS_01509 | SCR_011940 | 2026-02-07 02:08:27 | 40 | ||||||||||
|
MEGAN Resource Report Resource Website 1000+ mentions |
MEGAN (RRID:SCR_011942) | MEGAN | software resource | Software for analyzing metagenomes. | is listed by: OMICtools | OMICS_01516 | SCR_011942 | 2026-02-07 02:08:19 | 1338 | ||||||||||
|
MOCAT Resource Report Resource Website 10+ mentions |
MOCAT (RRID:SCR_011943) | MOCAT | software resource | Software package for analyzing metagenomics datasets. |
is listed by: OMICtools has parent organization: European Molecular Biology Laboratory |
OMICS_01517 | SCR_011943 | 2026-02-07 02:08:27 | 41 | ||||||||||
|
pyGCluster Resource Report Resource Website 1+ mentions |
pyGCluster (RRID:SCR_011944) | pyGCluster | software resource | A clustering algorithm focusing on noise injection for subsequent cluster validation. | is listed by: OMICtools | PMID:24177716 | OMICS_01573 | SCR_011944 | 2026-02-07 02:08:19 | 1 | |||||||||
|
ARTIVA Resource Report Resource Website |
ARTIVA (RRID:SCR_011946) | ARTIVA | software resource | Algorithm available in a R package that is a statistical framework to infer time-varying structures of gene-regulation networks. | r | is listed by: OMICtools | PMID:20860793 | Free, Public | OMICS_01680 | SCR_011946 | Auto Regressive TIme VArying regulatory models | 2026-02-07 02:08:25 | 0 | ||||||
|
Phrap Resource Report Resource Website 100+ mentions |
Phrap (RRID:SCR_011917) | Phrap | software resource | A software program for assembling shotgun DNA sequence data. | is listed by: OMICtools | Free to academic users | OMICS_01429 | SCR_011917 | 2026-02-07 02:08:24 | 369 | |||||||||
|
Ray Meta Resource Report Resource Website 10+ mentions |
Ray Meta (RRID:SCR_011918) | Ray Meta | software resource | Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23259615 | Free | OMICS_01431 | SCR_011918 | 2026-02-07 02:08:19 | 12 | |||||||
|
BLAT Resource Report Resource Website 1000+ mentions |
BLAT (RRID:SCR_011919) | BLAT | software resource | Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. | bio.tools |
is used by: deFuse is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA is required by: RelocaTE |
biotools:blat, OMICS_01434 | https://bio.tools/blat | SCR_011919 | 2026-02-07 02:08:27 | 3674 | ||||||||
|
HP Public Cloud Resource Report Resource Website 1+ mentions |
HP Public Cloud (RRID:SCR_011873) | HP Public Cloud | service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2019. Delivers public cloud infrastructure that''s business grade, open source-based, and developer focused., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cloud, computing, storage, platform | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01205 | SCR_011873 | 2026-02-07 02:08:23 | 2 | ||||||||
|
Joyent Resource Report Resource Website |
Joyent (RRID:SCR_011874) | Joyent | service resource | High-performance cloud infrastructure and big data analytics company, offering organizations of any size the best public and hybrid cloud infrastructure for today''s demanding real-time web and mobile applications. | cloud, big data | is listed by: OMICtools | For a fee | OMICS_01206 | SCR_011874 | 2026-02-07 02:08:17 | 0 | ||||||||
|
BBSeq Resource Report Resource Website 1+ mentions |
BBSeq (RRID:SCR_011877) | BBSeq | software resource | A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
biotools:bbseq, OMICS_01300 | https://bio.tools/bbseq | SCR_011877 | 2026-02-07 02:08:17 | 3 | ||||||||
|
IDBA-UD Resource Report Resource Website 100+ mentions |
IDBA-UD (RRID:SCR_011912) | IDBA-UD | software resource | Software for an iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. |
is listed by: OMICtools is listed by: Debian is related to: Meta-IDBA |
PMID:22495754 DOI:10.1093/bioinformatics/bts174 |
Acknowledgement requested | OMICS_01423 | https://sources.debian.org/src/idba/ | SCR_011912 | 2026-02-07 02:08:18 | 496 | |||||||
|
Meta-IDBA Resource Report Resource Website 1+ mentions |
Meta-IDBA (RRID:SCR_011913) | Meta-IDBA | software resource | Software for an iterative De Bruijn Graph De Novo short read assembler specially designed for de novo metagenomic assembly. (Please note that MetaIDBA is out of maintainance now, we recommend using IDBA-UD instead which generally performs better.) |
is listed by: OMICtools is related to: IDBA-UD |
PMID:21685107 | Acknowledgement requested | OMICS_01425 | SCR_011913 | 2026-02-07 02:08:26 | 9 |
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.
