Searching the RRID Resource Information Network
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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ProteinProphet Resource Report Resource Website 10+ mentions |
ProteinProphet (RRID:SCR_000286) | software resource | Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:14632076 | OMICS_02521, biotools:proteinprophet | https://bio.tools/proteinprophet | SCR_000286 | 2026-02-14 01:59:40 | 10 | ||||||||
|
GraphPad Resource Report Resource Website 1000+ mentions |
GraphPad (RRID:SCR_000306) | commercial organization | A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs. | company, data, graph, scientific, statistical, analysis, curve, fitting |
is listed by: SoftCite is parent organization of: GraphPad Prism |
Restricted | nlx_156835 | SCR_000306 | 2026-02-14 01:59:42 | 1284 | |||||||||
|
RStudio Resource Report Resource Website 1000+ mentions |
RStudio (RRID:SCR_000432) | RStudio | software resource | Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux). | R, statistical, computing, environment |
is used by: PlotsOfData is listed by: Debian is listed by: SoftCite is related to: rSPRITE is related to: shinyCircoss is parent organization of: Shiny is required by: circlncRNAnet |
Restricted | SciRes_000113 | https://sources.debian.org/src/rstudio/ https://posit.co/download/rstudio-desktop/ |
http://www.rstudio.com/ | SCR_000432 | 2026-02-14 01:59:45 | 1034 | ||||||
|
beadarray Resource Report Resource Website 100+ mentions |
beadarray (RRID:SCR_001314) | beadarray | software resource | Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. | microarray, quality control, one channel, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
PMID:17586828 | GNU General Public License, v2 | OMICS_02021, biotools:beadarray | https://bio.tools/beadarray | SCR_001314 | beadarray - Quality assessment and low-level analysis for Illumina BeadArray data | 2026-02-14 02:00:00 | 119 | |||||
|
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 | 2026-02-14 02:02:58 | 10 | |||||||||||
|
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 | 2026-02-14 02:02:16 | 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 | 2026-02-14 02:02:17 | 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 | 2026-02-14 02:02:48 | 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 | 2026-02-14 02:02:47 | 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 | 2026-02-14 02:02:52 | 2742 | ||||||||
|
GBrowse Resource Report Resource Website 10+ mentions |
GBrowse (RRID:SCR_006829) | GBrowse | data or information resource, database | A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions. | genome, annotation, database, perl, virus, dna, protein, reference sequence, chromosome, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: WormBase is related to: FlyBase is related to: International HapMap Project has parent organization: Generic Model Organism Database Project has parent organization: Indiana University; Indiana; USA |
Howard Hughes Medical Institute ; NHGRI HG00739; NHGRI P41HG02223 |
PMID:19957275 PMID:18428797 PMID:12368253 PMID:21400697 PMID:20194461 PMID:19357095 DOI:10.1002/0471250953.bi0909s28 |
The community can contribute to this resource, Requires Perl 5.8.6 or higher and the Apache web server | OMICS_00910, biotools:gbrowse, nif-0000-30597 | http://gmod.org/wiki/GBrowse https://bio.tools/gbrowse https://sources.debian.org/src/gbrowse/ |
SCR_006829 | Generic Genome Browser | 2026-02-14 02:06:35 | 43 | ||||
|
piRNABank Resource Report Resource Website 100+ mentions |
piRNABank (RRID:SCR_007858) | data or information resource, database | A web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals. It compiles all the possible clusters of piRNAs and also depicts piRNAs along with the associated genomic elements like genes and repeats on a genome wide map. piRNABank mainly provides data onnamely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila.Search options have been designed to query and obtain useful data from this online resource. It also facilitates abstraction of sequences and structural features from piRNA data. piRNABank provides the following features: * Simple search * Search piRNA clusters * Search homologous piRNAs * piRNA visualization map * Analysis tools, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | FASEB list | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03293 | SCR_007858 | piRNABank | 2026-02-14 02:06:09 | 163 | ||||||||
|
PREFAB Resource Report Resource Website 1+ mentions |
PREFAB (RRID:SCR_001009) | PREFAB | data or information resource, database | Downloadable data designed for testing multiple sequence alignment methods. | database, downloadable data, sequence alignment, sequence alignment method |
is listed by: OMICtools is listed by: SoftCite is related to: MUSCLE |
PMID:15034147 | Free, Available for download, Freely available | OMICS_00984 | SCR_001009 | PREFAB - Protein Reference Alignment Benchmark, Protein Reference Alignment Benchmark | 2026-02-14 02:06:00 | 1 | ||||||
|
Gemma Resource Report Resource Website 1000+ mentions |
Gemma (RRID:SCR_008007) | Gemma | data or information resource, database | Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results. | chip, microarray, functional genomics, gene expression, coexpression, differential expression, FASEB list |
is used by: NIF Data Federation is used by: Integrated Data Annotation is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: Gene Expression Omnibus is related to: Phenocarta has parent organization: University of British Columbia; British Columbia; Canada is parent organization of: Neurocarta |
NIGMS GM076990; Canadian Foundation for Innovation ; Michael Smith Foundation for Health Research ; Canadian Institutes for Health Research |
PMID:22782548 | Free, Freely available | nif-0000-08127, r3d100012747 | https://sources.debian.org/src/gemma/ https://doi.org/10.17616/R36R54 https://doi.org/10.17616/R36R54 |
SCR_008007 | 2026-02-14 02:06:41 | 1112 | |||||
|
Ingenuity Pathways Knowledge Base Resource Report Resource Website 1000+ mentions |
Ingenuity Pathways Knowledge Base (RRID:SCR_008117) | data or information resource, database | A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base . | gene, life science, molecule, protein, research, software, ontology, knowledge base, FASEB list |
is used by: Ingenuity Pathway Analysis is listed by: SoftCite has parent organization: QIAGEN |
Available to the research community, Commercial | nif-0000-20858 | SCR_008117 | Ingenuity Knowledge Base | 2026-02-14 02:06:33 | 4627 | ||||||||
|
PostgreSQL Resource Report Resource Website 100+ mentions |
PostgreSQL (RRID:SCR_021067) | data or information resource, database | Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems. | Object relational database system, SQL language, data storage, data, database system |
uses: pgAdmin is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | SCR_021067 | Postgres | 2026-02-14 02:06:33 | 108 | |||||||||
|
Scopus Resource Report Resource Website 100+ mentions |
Scopus (RRID:SCR_022559) | data or information resource, database | Abstract and indexing database with full text links that is produced by Elsevier Co. Combines expertly curated abstract and citation database with enriched data and linked scholarly literature across wide variety of disciplines. | Elsevier Co, abstract and citation database, data, scholarly literature, abstract and indexing database, full text links | is listed by: SoftCite | PMID:16522216 | SCR_022559 | 2026-02-14 02:06:56 | 324 | ||||||||||
|
ANALYZE Resource Report Resource Website 1000+ mentions |
ANALYZE (RRID:SCR_009120) | ANALYZE | software application, software resource | A set of useful accessory programs to the LINKAGE package. It simplifies the performance of a large array of parametric and nonparametric tests for linkage and association on data entered in LINKAGE format pedigree and parameter files. (entry from Genetic Analysis Software) | gene, genetic, genomic, pascal, unix, sunos, solaris, osf1 |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154223 | SCR_009120 | 2026-02-15 09:19:38 | 1102 | |||||||||
|
QUANTO Resource Report Resource Website 500+ mentions |
QUANTO (RRID:SCR_009084) | QUANTO | software application, software resource | Software program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs. Quanto is a 32-bit Windows application requiring Windows 95, 98, NT, 2000, ME or XP to run. The graphical user interface allows th e user to easily change the model and view the results without having to edit an input file and rerun the program for every model. The results of a session are stored to a log file. This log can be printed or saved to a file for reviewing at a later date. An option is included to create a text file of the log that can be imported into other documents. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, (98/nt/2000/..) |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154095 | SCR_009084 | 2026-02-15 09:19:37 | 915 | |||||||||
|
IMPUTE Resource Report Resource Website 500+ mentions |
IMPUTE (RRID:SCR_009245) | IMPUTE | software application, software resource | Software application for estimating (imputing) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. (entry from Genetic Analysis Software) | gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154411 | SCR_009245 | 2026-02-15 09:20:06 | 628 |
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