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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GenePix Pro Resource Report Resource Website 500+ mentions |
GenePix Pro (RRID:SCR_010969) | GenePix Pro | software resource | Industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and intuitive workflows. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00840 | SCR_010969 | 2026-08-01 12:04:19 | 627 | ||||||||||
|
GenomeStudio Resource Report Resource Website 1000+ mentions |
GenomeStudio (RRID:SCR_010973) | GenomeStudio | software resource | Visualize and analyze data generated by all of Illumina''s platforms. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00854 | SCR_010973 | 2026-08-01 12:04:18 | 2954 | ||||||||||
|
ComBat Resource Report Resource Website 1000+ mentions |
ComBat (RRID:SCR_010974) | ComBat | software resource | Adjusting batch effects in microarray expression data using Empirical Bayes methods. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00857 | SCR_010974 | 2026-08-01 12:04:19 | 3492 | ||||||||||
|
BASE Resource Report Resource Website 500+ mentions |
BASE (RRID:SCR_010937) | BASE | software resource | A comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Lund University; Lund; Sweden |
PMID:19822003 | GNU General Public License, v3 | OMICS_00749 | SCR_010937 | BASE - BioArray Software Environment, BioArray Software Environment | 2026-08-01 12:04:01 | 506 | |||||||
|
BRB-ArrayTools Resource Report Resource Website 500+ mentions |
BRB-ArrayTools (RRID:SCR_010938) | BRB-ArrayTools | software resource | An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00750, biotools:brb-arraytools | https://bio.tools/brb-arraytools | SCR_010938 | 2026-08-01 12:04:18 | 569 | |||||||
|
BioExtract Resource Report Resource Website 10+ mentions |
BioExtract (RRID:SCR_005397) | BioExtract | service resource | An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. | nucleotide sequence, protein sequence, viridiplantae, viridiplantae protein, nucleotide, sequence, protein, viridiplantae, workflow, software, database, bioinformatics, platform, genome, genomic analysis, analytic tool |
is listed by: OMICtools is listed by: SoftCite is related to: NCBI Nucleotide is related to: NCBI Protein Database is related to: UniProt is related to: UniRef is related to: EMBOSS is related to: BioMoby is related to: KEGG has parent organization: Indiana University; Indiana; USA has parent organization: University of South Dakota; South Dakota; USA |
NSF 0090732; NSF IOS-1126481 |
PMID:21546552 PMID:20865520 PMID:20150665 PMID:20054995 |
OMICS_01138 | SCR_005397 | BioExtract Server | 2026-08-01 12:02:51 | 11 | ||||||
|
Hydra Resource Report Resource Website 100+ mentions |
Hydra (RRID:SCR_005260) | Hydra | software resource | Software that detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose signatures corroborate the same putative breakpoint. Hydra can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments. Hydra does not attempt to classify SV breakpoints based on the mapping distances and orientations of each breakpoint cluster, it merely detects and reports breakpoints. This is an intentional decision, as it was observed that in loci affected by complex rearrangements, the type of variant suggested by the breakpoint signature is not always correct. Hydra does report the orientations, distances, number of supporting read-pairs, etc., for each breakpoint. It is suggested that downstream methods be used to classify variants based on the genomic features that they overlap and the co-occurrence of other breakpoints. For example, they developed BEDTools for exactly this purpose and the breakpoints reported by Hydra are in the BEDPE format used by BEDTools. Future releases of Hydra will include scripts that assist in the classification process. | structural variation, genome, genomic, breakpoint, c++, cnv, pem, paired-end, segmental duplication, rearrangement |
is listed by: OMICtools is listed by: SoftCite is related to: BEDTools has parent organization: Google Code has parent organization: University of Virginia; Virginia; USA |
OMICS_00318 | SCR_005260 | hydra-sv | 2026-08-01 12:02:58 | 115 | ||||||||
|
PASS Resource Report Resource Website 1000+ mentions |
PASS (RRID:SCR_005490) | PASS | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 19, 2020.A program to align short sequences that has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by ILLUMINA, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: PASS-bis has parent organization: University of Padua; Padua; Italy |
PMID:19218350 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pass, OMICS_00673 | https://bio.tools/pass | SCR_005490 | PASS: a program to align short sequences | 2026-08-01 12:02:55 | 2085 | |||||
|
Maq Resource Report Resource Website 50+ mentions |
Maq (RRID:SCR_005485) | Maq | software resource | A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way. | command-line, curses/ncurses, opengl, c, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License, v2 | biotools:maq, OMICS_00668 | https://bio.tools/maq, https://sources.debian.org/src/maq/ | SCR_005485 | mapass2, Mapping and Assembly with Quality, Mapping and Assembly with Qualities, Maq: Mapping and Assembly with Qualities | 2026-08-01 12:02:59 | 69 | |||||
|
AutoDock Resource Report Resource Website 10000+ mentions |
AutoDock (RRID:SCR_012746) | autodock | software resource | Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids. | Small molecules receptor binding, automated docking tools, 3D structure, AutoDock 4, AutoDock Vina, ligand, docking |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Autogrid |
PMID:19399780 | Free, Available for download, Freely available | OMICS_01594, biotools:autodock | https://bio.tools/autodock, https://sources.debian.org/src/autodock/ | SCR_012746 | 2026-08-01 12:04:39 | 11935 | ||||||
|
ChIPpeakAnno Resource Report Resource Website 100+ mentions |
ChIPpeakAnno (RRID:SCR_012828) | ChIPpeakAnno | software resource | Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00804 | SCR_012828 | 2026-08-01 12:04:52 | 448 | ||||||||||
|
RepeatMasker Resource Report Resource Website 5000+ mentions |
RepeatMasker (RRID:SCR_012954) | software resource | Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ). |
uses: Repbase uses: RMBlast is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
DOI:10.1007/978-1-61779-603-6_2 | nlx_156840, OMICS_09436 | https://sources.debian.org/src/repeatmasker/ | SCR_012954 | repeatmasker.org | 2026-08-01 12:04:42 | 9750 | ||||||||
|
Trans-ABySS Resource Report Resource Website 50+ mentions |
Trans-ABySS (RRID:SCR_013322) | Trans-ABySS | software resource | A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
OMICS_01326, biotools:trans-abyss | https://bio.tools/trans-abyss/ | SCR_013322 | 2026-08-01 12:04:58 | 69 | ||||||||
|
TreeView Resource Report Resource Website 1000+ mentions |
TreeView (RRID:SCR_013503) | TreeView | software resource | Software to graphically browse results of clustering and other analyses from Cluster. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1093/bioinformatics/bth349 | OMICS_01574 | https://sources.debian.org/src/treeview/ | SCR_013503 | 2026-08-01 12:04:49 | 2742 | ||||||||
|
Integrative Genomics Viewer Resource Report Resource Website 500+ mentions |
Integrative Genomics Viewer (RRID:SCR_011793) | IGV | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. | genomic datasets exploration, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
DOI:10.1038/nbt.1754 | OMICS_00917, biotools:igv | https://bio.tools/igv, https://sources.debian.org/src/igv/ | SCR_011793 | 2026-08-01 12:04:30 | 809 | |||||||
|
Definiens Developer XD Resource Report Resource Website 10+ mentions |
Definiens Developer XD (RRID:SCR_014283) | software resource | A development environment designed to create automated image analysis solutions for segmentation and classification tasks. It delivers quantitative and consistent data for any type of image (e.g., IHC, ISH, IF images in different formats). Developer XD also contains a large library of image analysis algorithms, which users can add to, for whole slide images and tissue microarrays (TMAs). It can be integrated with an existing Tissue Studio installation. | development environment, image analysis solution, segmentation, classification, image analysis algorithm library, tissue microarray, whole slide image, tissue studio | is listed by: SoftCite | SCR_014283 | 2026-08-01 12:05:00 | 10 | |||||||||||
|
UCHIME Resource Report Resource Website 1000+ mentions |
UCHIME (RRID:SCR_008057) | UCHIME | software resource | An algorithm for detecting chimeric sequences. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_01115 | SCR_008057 | 2026-08-01 12:03:37 | 1777 | ||||||||||
|
Scion Image Resource Report Resource Website 5000+ mentions |
Scion Image (RRID:SCR_008673) | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Commercial software vendor. | imaging, industrial, scientific | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33408 | SCR_008673 | 2026-08-01 12:03:50 | 5759 | |||||||||
|
Primer Designer Resource Report Resource Website 1+ mentions |
Primer Designer (RRID:SCR_003189) | Primer Designer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki. | primer, primer design |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02327 | https://www.thermofisher.com/us/en/home/life-science/oligonucleotides-primers-probes-genes/custom-dna-oligos/oligo-design-tools.html?ef_id=Cj0KCQjw-NfDBhDyARIsAD-ILeBszOXU4wXumqZJ--N8Z5rguB5P2-7UmpEuidzHsK1sgSXJROQ3of8aAtkqEALw_wcB:G:s&s_kwcid=AL!3652!3!683518170873!e!!g!!primer%20designer!20841448243!155985486683&cid=bid_mol_pch_r01_co_cp1358_pjt0000_bid00000_0se_gaw_nt_pur_con&gad_source=1&gad_campaignid=20841448243&gbraid=0AAAAADxi_GTCU-6xCgQrctnmtmtMSDEQj&gclid=Cj0KCQjw-NfDBhDyARIsAD-ILeBszOXU4wXumqZJ--N8Z5rguB5P2-7UmpEuidzHsK1sgSXJROQ3of8aAtkqEALw_wcB | SCR_003189 | 2026-08-01 12:02:28 | 2 | |||||||
|
RevMan Resource Report Resource Website 10000+ mentions |
RevMan (RRID:SCR_003581) | RevMan | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00244 | SCR_003581 | Review Manager | 2026-08-01 12:02:31 | 12961 |
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 ASWG Resources search. From here you can search through a compilation of resources used by ASWG and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that ASWG 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 ASWG then you can log in from here to get additional features in ASWG 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 ASWG 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 ASWG Community.
Our Information
