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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | data or information resource, database, service resource, storage service resource, data repository | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem, https://doi.org/10.17616/R3GW37 | SCR_004284 | 2026-08-08 11:58:19 | 15598 | ||||||
|
InsertionMapper Resource Report Resource Website |
InsertionMapper (RRID:SCR_004163) | InsertionMapper | software resource | A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences. | high throughput sequencing, dna sequence, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Montclair State University; New Jersey; USA |
PMID:24090499 | Acknowledgement requested, GNU General Public License | OMICS_01547, biotools:insertionmapper | https://bio.tools/insertionmapper | SCR_004163 | 2026-08-08 11:58:18 | 0 | ||||||
|
bcbio-nextgen Resource Report Resource Website 100+ mentions |
bcbio-nextgen (RRID:SCR_004316) | bcbio-nextgen | software resource | A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:bcbio-nextgen, OMICS_01121, BioTools:bcbio-nextgen | https://github.com/chapmanb/bcbb/blob/master/nextgen/README.md, https://bio.tools/bcbio-nextgen, https://bio.tools/bcbio-nextgen | SCR_004316 | 2026-08-08 11:58:20 | 165 | |||||||
|
TagDust Resource Report Resource Website 50+ mentions |
TagDust (RRID:SCR_004175) | TagDust | software resource | A program to eliminate artifactual reads from next-generation sequencing data sets. | unix/linux, bio.tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:19737799 | biotools:tagdust, OMICS_01095, biotools:nexalign | https://bio.tools/tagdust, https://bio.tools/nexalign | SCR_004175 | 2026-08-08 11:58:16 | 55 | |||||||
|
Mercury Resource Report Resource Website 500+ mentions |
Mercury (RRID:SCR_004231) | Mercury | software resource | An automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. The analysis pipeline is deployed in local hardware and the Amazon Web Services cloud via the DNAnexus platform. | next-generation sequencing, genome, cloud, exome, cloud computing, illumina, bam, variant call file |
is listed by: OMICtools is related to: Amazon Web Services has parent organization: Baylor College of Medicine Human Genome Sequencing Center |
PMID:24475911 | OMICS_02290 | SCR_004231 | Illumina Mercury pipeline | 2026-08-08 11:58:18 | 989 | |||||||
|
CB-Commander Resource Report Resource Website |
CB-Commander (RRID:SCR_004237) | CB-Commander | software resource | A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline. | java, java swing, high throughput sequencing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
GNU General Public License, v2 | OMICS_01534 | http://sourceforge.net/projects/cb-commander/ | SCR_004237 | 2026-08-08 11:58:17 | 0 | |||||||
|
Artemis: Genome Browser and Annotation Tool Resource Report Resource Website 100+ mentions |
Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) | Artemis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | training tool, genome browser, gene annotation, java, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: DNAPlotter has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom works with: Alien-hunter |
Wellcome Trust | PMID:11120685 DOI:10.1093/bioinformatics/btr703 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_28554, OMICS_00903, biotools:artemis | https://bio.tools/artemis, https://sources.debian.org/src/art-nextgen-simulation-tools/ | SCR_004267 | 2026-08-08 11:58:14 | 422 | |||||
|
PeaKDEck Resource Report Resource Website 10+ mentions |
PeaKDEck (RRID:SCR_004268) | PeaKDEck | software resource | A peak-calling software program for DNAseI-seq data. | perl, command line, gui |
is listed by: OMICtools has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:24407222 | OMICS_02207 | SCR_004268 | 2026-08-08 11:58:18 | 10 | ||||||||
|
DER Finder Resource Report Resource Website 1+ mentions |
DER Finder (RRID:SCR_004250) | DER Finder | software toolkit, software library, software resource, software application, data processing software | R package for differential expression analysis of RNA-seq data. | differential expression, rna-seq, false discovery rate, genomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24398039 | Free, Public | biotools:derfinder, OMICS_02208 | https://bio.tools/derfinder | SCR_004250 | derfinder | 2026-08-08 11:58:13 | 5 | |||||
|
TFBS Resource Report Resource Website 10+ mentions |
TFBS (RRID:SCR_015774) | software resource, software application, data analysis software, data processing software | Perl software for transcription factor binding site detection and analysis. It implements classes for the representation of objects encountered in analysis of these protein-binding sites. | protein-binding, transcription factor, factor binding, binding site detection, transcription analysis, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:12176838 DOI:10.1093/bioinformatics/18.8.1135 |
Free, Available for download, No longer in development | biotools:tfbs, OMICS_20526 | https://github.com/ComputationalRegulatoryGenomicsICL/TFBS, https://bio.tools/tfbs, https://sources.debian.org/src/libtfbs-perl/ | SCR_015774 | 2026-08-08 12:00:44 | 44 | |||||||
|
Ariba Resource Report Resource Website 100+ mentions |
Ariba (RRID:SCR_015976) | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. | software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlst |
is listed by: Debian is listed by: OMICtools |
Wellcome Trust 206194; Biotechnology and Biological Sciences Research Council BB/M014088/1 |
PMID:29177089 DOI:10.1099/mgen.0.000131 |
Free, Available for download, Freely available | OMICS_17327 | https://sources.debian.org/src/artemis/ | SCR_015976 | 2026-08-08 12:00:45 | 220 | ||||||
|
Atac Resource Report Resource Website 1000+ mentions |
Atac (RRID:SCR_015980) | sequence analysis software, image analysis software, software resource, software application, data analysis software, alignment software, data processing software | Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences. | software, tool, DNA, sequence, analysis, aligning, genome, compare, mapping, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btr285 | Free, Freely available, Available for download | OMICS_29044, biotools:atac | https://bio.tools/atac, https://sources.debian.org/src/atac/ | SCR_015980 | 2026-08-08 12:00:45 | 1826 | |||||||
|
BALLView Resource Report Resource Website 1+ mentions |
BALLView (RRID:SCR_015986) | software resource, software application, simulation software, standalone software, data visualization software, data processing software | Software for molecular visualization and modeling. It provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features. | molecular, modeling, visualization, application, computation, algorithm, library, bioinformatics |
is listed by: Debian is listed by: OMICtools |
Deutsche Forschungsgemeinschaft BIZ 1/1-3; BIZ 4/1-1 and LE 952/2-3 |
PMID:16332707 DOI:10.1093/bioinformatics/bti818 |
Free, Freely available, Free for download, Runs on Mac OS, Runs on Windows | OMICS_05049 | https://github.com/BALL-Project/ball/wiki/Tutorials, https://sources.debian.org/src/bamtools/ | SCR_015986 | BALL:Biochemical Algorithms Library, Biochemical Algorithms Library | 2026-08-08 12:00:27 | 4 | |||||
|
Axe Resource Report Resource Website 1+ mentions |
Axe (RRID:SCR_015984) | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples. | software, tool, sequence, analysis, barcode, demultiplexing |
is listed by: Debian is listed by: OMICtools |
Free, Freely available, Available for download | OMICS_19788 | https://readthedocs.org/projects/axe-demultiplexer/, https://sources.debian.org/src/baitfisher/ | SCR_015984 | Axe-demultiplexer | 2026-08-08 12:00:45 | 1 | |||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | software toolkit, software resource, software application, data management software, data analysis software, data processing software | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools, https://sources.debian.org/src/bamtools/ | SCR_015987 | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-08-08 12:00:45 | 344 | ||||||
|
ALTER Resource Report Resource Website 100+ mentions |
ALTER (RRID:SCR_015968) | web application, sequence analysis software, image analysis software, software resource, software application, data analysis software, alignment software, data processing software | Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats. | Alignment conversion, genome, sequence, DNA, protein, format alignment, phylogenetics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ERC-2007-Stg 203161-PHYGENOM to D.P.; Spanish Ministry of Science and Education BFU2009-08611 to D.P.; Xunta de Galicia PGIDIT07PXIB310202PR to D.P.; INBIOMED initiative ; University of Vigo 09VIB10 to F.F-.R. |
PMID:20439312 DOI:10.1093/nar/gkq321 |
Freely available, Free, Available for download | OMICS_19786, biotools:alter | https://github.com/sing-group/ALTER, https://bio.tools/alter, https://sources.debian.org/src/alter-sequence-alignment/ | SCR_015968 | ALTER: ALignment Transformation EnviRonment, ALignment Transformation EnviRonment | 2026-08-08 12:00:27 | 125 | |||||
|
AMAP Resource Report Resource Website 100+ mentions |
AMAP (RRID:SCR_015969) | image analysis software, software resource, software application, source code, alignment software, data processing software | Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method. | software, peptide, sequence, alignment, annealing, bioinformatics, multiple, svn, posterior, decoding |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NSF EF 03-31494; NHGRI R01 HG2362; NSF CCF0347992 |
PMID:17237099 DOI:10.1093/bioinformatics/btl311 |
Free, Available for download | OMICS_19787 | http://baboon.math.berkeley.edu/amap/, https://sources.debian.org/src/amap-align/ | https://sources.debian.org/src/amos-assembler/ | SCR_015969 | amap-align | 2026-08-08 12:00:45 | 400 | ||||
|
Aragorn Resource Report Resource Website 100+ mentions |
Aragorn (RRID:SCR_015974) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software that detects tRNA genes and tmRNA genes in nucleotide sequences. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | software, program, nucleotide, sequence, detect, tmRNA, tRNA |
is listed by: Debian is listed by: OMICtools |
PMID:14704338 DOI:10.1093/nar/gkh152 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04227 | https://sources.debian.org/src/arden/ | SCR_015974 | 2026-08-08 12:00:46 | 474 | |||||||
|
Arden Resource Report Resource Website 10+ mentions |
Arden (RRID:SCR_015975) | software toolkit, image analysis software, software resource, software application, source code, alignment software, data processing software | Software for specificity control of read alignments using an artificial reference. It estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation. | software, alignment, artificial, reference, estimate, error, genome, false, positive, next, generation, sequencing, DNA, python |
is listed by: Debian is listed by: OMICtools |
Robert Koch-Institute (RKI) | PMID:23685787 DOI:10.1093/bioinformatics/btt255 |
Free, Freely available | OMICS_09783 | https://sources.debian.org/src/ariba/ | SCR_015975 | ARDEN: Artificial Reference Driven Estimation of false positives in NGS data, Artificial Reference Driven Estimation of false positives in NGS data | 2026-08-08 12:00:27 | 49 | |||||
|
DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search. | sequence, aligner, high, performance, analysis, big, data, protein, DNA, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
PMID:25402007 DOI:10.1038/nmeth.3176 |
Free, Available for download | OMICS_08011, biotools:diamond | https://bio.tools/diamond, https://sources.debian.org/src/diamond-aligner/ | SCR_016071 | 2026-08-08 12:00:48 | 489 |
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.
