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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Mega BLAST Resource Report Resource Website 100+ mentions |
Mega BLAST (RRID:SCR_011920) | Mega BLAST | software resource | Software that uses the greedy algorithm for nucleotide sequence alignment search. |
is listed by: OMICtools has parent organization: NCBI |
OMICS_01435 | SCR_011920 | 2026-08-08 11:59:55 | 281 | ||||||||||
|
UCLUST algorithm Resource Report Resource Website 50+ mentions |
UCLUST algorithm (RRID:SCR_011921) | UCLUST | software resource | Algorithm that divides a set of sequences into clusters | is listed by: OMICtools | PMID:20709691 | OMICS_01448 | SCR_011921 | 2026-08-08 12:00:02 | 57 | |||||||||
|
eXPatGen Resource Report Resource Website |
eXPatGen (RRID:SCR_011922) | eXPatGen | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A simulator of gene expression patterns in order to evaluate different analysis methods, such as clustering and principle component analysis (PCA). | is listed by: OMICtools | PMID:12801875 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01572 | SCR_011922 | eXPatGen - An On-line Gene Expression Pattern Generator | 2026-08-08 11:59:37 | 0 | |||||||
|
EBARDenovo Resource Report Resource Website 1+ mentions |
EBARDenovo (RRID:SCR_011890) | EBARDenovo | software resource | Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01317 | SCR_011890 | 2026-08-08 12:00:01 | 2 | ||||||||||
|
IDBA-Tran Resource Report Resource Website 10+ mentions |
IDBA-Tran (RRID:SCR_011891) | IDBA-Tran | software resource | An iterative De Bruijn Graph De Novo short read assembler for transcriptome. | is listed by: OMICtools | OMICS_01318 | SCR_011891 | 2026-08-08 11:59:37 | 26 | ||||||||||
|
NextGENe Resource Report Resource Website 100+ mentions |
NextGENe (RRID:SCR_011859) | NextGENe | software resource, software application, data analysis software, data processing software | Software tool for Next Generation sequence analysis. Analytical partner for analysis of desktop sequencing data produced by Illumina iSeq, Miniseq, MiSeq, NextSeq, HiSeq, and NovaSeq systems, Ion Torrent Ion GeneStudio S5, PGM, and Proton systems as well as other platforms. Software runs on Windows Operating System, which provides biologist friendly interface. It does not require scripting or other bioinformatics support. | Next Generation Sequence Analysis, desktop sequencing data analysis, sequencing data | is listed by: OMICtools | Commercial license | OMICS_01131 | http://softgenetics.com/NextGENe.html | SCR_011859 | Next GENeration Sequence Analysis | 2026-08-08 11:59:36 | 381 | ||||||
|
RACER Resource Report Resource Website 10+ mentions |
RACER (RRID:SCR_011852) | RACER | software resource | A software program for correcting errors in sequencing data. | is listed by: OMICtools | OMICS_01108 | SCR_011852 | 2026-08-08 11:59:54 | 37 | ||||||||||
|
TIGRESS Resource Report Resource Website 1+ mentions |
TIGRESS (RRID:SCR_011977) | TIGRESS | software resource | Software providing a scoring technique for stability selection, which improves the performance of feature selection with LARS. TIGRESS can be run online through the GenePattern platform (GP-DREAM, http://dream.broadinstitute.org). | matlab |
is listed by: OMICtools is related to: GenePattern |
PMID:23173819 | OMICS_01687 | SCR_011977 | Trustful Inference of Gene REgulation using Stability Selection, TIGRESS: Trustful Inference of Gene REgulation using Stability Selection | 2026-08-08 11:59:55 | 9 | |||||||
|
NARWHAL Resource Report Resource Website 10+ mentions |
NARWHAL (RRID:SCR_011858) | NARWHAL | software resource | Automates the primary analysis of massive parallel sequencing data. |
is listed by: OMICtools has parent organization: Netherlands Bioinformatics Centre |
OMICS_01130 | SCR_011858 | 2026-08-08 12:00:00 | 10 | ||||||||||
|
orthAgogue Resource Report Resource Website 10+ mentions |
orthAgogue (RRID:SCR_011979) | orthAgogue | software resource | A software tool for high speed estimation of homology relations within and between species in massive data sets. | unix/linux |
is listed by: OMICtools has parent organization: Google Code |
PMID:24115168 | GNU General Public License, v3 | OMICS_01691 | SCR_011979 | orthAgogue: a tool for high speed estimation of homology relations within and between species in massive data sets. | 2026-08-08 12:00:03 | 32 | ||||||
|
SeqGene Resource Report Resource Website 1+ mentions |
SeqGene (RRID:SCR_011861) | SeqGene | software resource | An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc. |
is listed by: OMICtools has parent organization: SourceForge |
Open unspecified license | OMICS_01134 | SCR_011861 | 2026-08-08 11:59:54 | 2 | |||||||||
|
Oqtans Resource Report Resource Website |
Oqtans (RRID:SCR_011905) | Oqtans | software resource | It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis. | windows, illumina | is listed by: OMICtools | Apache License | OMICS_01407 | SCR_011905 | Online Quantitative Transcriptome Analysis | 2026-08-08 11:59:55 | 0 | |||||||
|
reddit Resource Report Resource Website 50+ mentions |
reddit (RRID:SCR_011983) | software resource | A subreddit dedicated to bioinformatics, computational genomics and systems biology. | is listed by: OMICtools | OMICS_01708 | SCR_011983 | 2026-08-08 11:59:56 | 95 | |||||||||||
|
Genboree Workbench Resource Report Resource Website |
Genboree Workbench (RRID:SCR_011864) | Genboree | service resource | Service where users are able to upload and store data, access bioinformatics tools, and perform analyses. | metagenome, visualization, genome, transcriptiome, cistrome, epigenome, analysis, rna-seq, chip-seq |
is listed by: OMICtools has parent organization: Baylor University; Texas; USA |
Free for academic use | OMICS_01142 | SCR_011864 | 2026-08-08 11:59:54 | 0 | ||||||||
|
Ibis Resource Report Resource Website 10+ mentions |
Ibis (RRID:SCR_011865) | Ibis | software resource | An accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads. | is listed by: OMICtools | OMICS_01151 | SCR_011865 | Improved base identification system | 2026-08-08 12:00:00 | 49 | |||||||||
|
naiveBayesCall Resource Report Resource Website |
naiveBayesCall (RRID:SCR_011866) | naiveBayesCall | software resource | An efficient model-based base-calling algorithm for high-throughput sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01152, biotools:bayescall | https://bio.tools/bayescall | SCR_011866 | 2026-08-08 11:59:36 | 0 | ||||||||
|
htseq-count Resource Report Resource Website 1000+ mentions |
htseq-count (RRID:SCR_011867) | htseq-count | software resource | Script distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: European Molecular Biology Laboratory |
PMID:23975260 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01162 | SCR_011867 | Counting reads in features | 2026-08-08 11:59:54 | 2601 | |||||||
|
RNAseqViewer Resource Report Resource Website 1+ mentions |
RNAseqViewer (RRID:SCR_011900) | RNAseqViewer | software resource | Software to visualize the various data from the RNA-Seq analyzing process, for single or multiple samples. | is listed by: OMICtools | PMID:24215023 | Free to academic users | OMICS_01363 | SCR_011900 | 2026-08-08 12:00:01 | 4 | ||||||||
|
ABNER Resource Report Resource Website 10+ mentions |
ABNER (RRID:SCR_011868) | ABNER | software resource | A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
biotools:abner, OMICS_01168 | https://bio.tools/abner | SCR_011868 | 2026-08-08 12:00:00 | 27 | ||||||||
|
Eoulsan Resource Report Resource Website 10+ mentions |
Eoulsan (RRID:SCR_011901) | Eoulsan | software resource | A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers. | matlab, unix/linux, mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22492314 | OMICS_01402, biotools:Eoulsan | https://www.outils.genomique.biologie.ens.fr/eoulsan/, https://bio.tools/Eoulsan | SCR_011901 | 2026-08-08 11:59:37 | 22 |
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.
