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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MDQC Resource Report Resource Website |
MDQC (RRID:SCR_001352) | MDQC | software resource | A multivariate quality assessment software for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality. | microarray, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:17933854 | Free, Available for download, Freely available | OMICS_01987 | SCR_001352 | Mahalanobis Distance Quality Control for microarrays | 2026-02-07 02:05:31 | 0 | ||||||
|
MACAT Resource Report Resource Website |
MACAT (RRID:SCR_001350) | MACAT | software resource | Software library that contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. It is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. | differential expression, microarray, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:15572464 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01989, biotools:macat | https://bio.tools/macat | SCR_001350 | MicroArray Chromosome Analysis Tool | 2026-02-07 02:05:36 | 0 | |||||
|
nnNorm Resource Report Resource Website |
nnNorm (RRID:SCR_001354) | nnNorm | software resource | Software package that allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01985 | SCR_001354 | nnNorm - Spatial and intensity based normalization of cDNA microarray data based on robust neural nets | 2026-02-07 02:05:30 | 0 | |||||||
|
maCorrPlot Resource Report Resource Website 1+ mentions |
maCorrPlot (RRID:SCR_001348) | maCorrPlot | software resource | Software that graphically displays correlation in microarray data that is due to insufficient normalization. | microarray, preprocessing, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:15799785 | Free, Available for download, Freely available | OMICS_01991 | SCR_001348 | maCorrPlot - Visualize artificial correlation in microarray data | 2026-02-07 02:05:30 | 2 | ||||||
|
lapmix Resource Report Resource Website |
lapmix (RRID:SCR_001347) | lapmix | software resource | Software to identify differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. | differential expression, microarray, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:lapmix, OMICS_01992 | https://bio.tools/lapmix | SCR_001347 | Laplace Mixture Model in Microarray Experiments | 2026-02-07 02:05:36 | 0 | ||||||
|
FARMS Resource Report Resource Website 10+ mentions |
FARMS (RRID:SCR_001344) | FARMS | software resource | Software using a model-based technique for summarizing high-density oligonucleotide array data at probe level for Affymetrix GeneChips. It is based on a factor analysis model for which a Bayesian maximum a posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise. | oligonucleotide array, probe, affymetrix genechip, r, unix, windows, microarray, summarization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johannes Kepler University of Linz; Linz; Austria |
PMID:16473874 | Free, Freely Available | OMICS_01995, biotools:farms | https://bio.tools/farms | SCR_001344 | Factor Analysis for Robust Microarray Summarization | 2026-02-07 02:05:36 | 28 | |||||
|
OCplus Resource Report Resource Website 1+ mentions |
OCplus (RRID:SCR_001342) | OCplus | software resource | Software package that allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). | differential expression, microarray, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16368770 | Free, Available for download, Freely available | OMICS_01999 | SCR_001342 | Ocplus - Operating characteristics plus sample size and local fdr for microarray experiments | 2026-02-07 02:05:30 | 1 | ||||||
|
bridge Resource Report Resource Website 100+ mentions |
bridge (RRID:SCR_001343) | bridge | software resource | Software package to test for differentially expressed genes with microarray data. It can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. The model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space. | cdna microarray, affymetrix chip, differential expression, microarray, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:16542223 | Free, Available for download, Freely available | OMICS_01996, biotools:bridge | http://www.bioconductor.org/packages/release/bioc/html/bridge.html | SCR_001343 | Bayesian Robust Inference for Differential Gene Expression | 2026-02-07 02:05:31 | 154 | |||||
|
CALIB Resource Report Resource Website 100+ mentions |
CALIB (RRID:SCR_001338) | CALIB | software resource | Software package that contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:17485432 | Free, Available for download, Freely available | OMICS_02003 | http://www.bioconductor.org/packages/release/bioc/html/CALIB.html | SCR_001338 | 2026-02-07 02:05:36 | 131 | ||||||
|
LPE Resource Report Resource Website |
LPE (RRID:SCR_001364) | LPE | software resource | Software library used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional "BH" or "BY" procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. | differential expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18450812 | Free, Available for download, Freely available | OMICS_01978 | SCR_001364 | Local Pooled Error | 2026-02-07 02:05:36 | 0 | ||||||
|
aroma.light Resource Report Resource Website 1+ mentions |
aroma.light (RRID:SCR_001312) | aroma.light | software resource | Light-weight software package for normalization and visualization of microarray data using only basic R data types. Software can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. | infrastructure, microarray, preprocessing, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
DOI:10.1186/1471-2105-11-245 | Free, Available for download, Freely available | OMICS_01998, biotools:aroma.light | https://bio.tools/aroma.light https://sources.debian.org/src/r-bioc-aroma.light/ |
SCR_001312 | 2026-02-07 02:05:29 | 1 | ||||||
|
BeadDataPackR Resource Report Resource Website |
BeadDataPackR (RRID:SCR_001310) | BeadDataPackR | software resource | Software that provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform. | microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:20981138 | Free, Available for download, Freely available | biotools:beaddatapackr, OMICS_02023 | https://bio.tools/beaddatapackr | SCR_001310 | BeadDataPackR - Compression of Illumina BeadArray data | 2026-02-07 02:05:35 | 0 | |||||
|
OLIN Resource Report Resource Website 10+ mentions |
OLIN (RRID:SCR_001304) | OLIN | software resource | Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data. | r, normalization, visualization, quality control, two-channel, microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:15585527 | Free, Available for download, Freely available | biotools:olin, OMICS_02029 | http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html | SCR_001304 | Optimised Local Intensity-dependent Normalisation | 2026-02-07 02:05:35 | 18 | |||||
|
qcmetrics Resource Report Resource Website 1+ mentions |
qcmetrics (RRID:SCR_001303) | qcmetrics | software resource | Software package that provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats. | mass spectrometry, microarray, proteomics, quality control, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02032, biotools:qcmetrics, BioTools:qcmetrics | https://bio.tools/qcmetrics https://bio.tools/qcmetrics https://bio.tools/qcmetrics |
SCR_001303 | qcmetrics - A Framework for Quality Control | 2026-02-07 02:05:30 | 1 | ||||||
|
DEXUS Resource Report Resource Website 1+ mentions |
DEXUS (RRID:SCR_001309) | DEXUS | software resource | Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power. | classification, differential expression, gene expression, hapmap, quality control, rna-seq, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24049071 | Free, Available for download, Freely available | biotools:dexus, OMICS_02024 | http://www.bioconductor.org/packages/release/bioc/html/dexus.html | SCR_001309 | DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates | 2026-02-07 02:05:30 | 1 | |||||
|
James Cook University; Townsville; Australia Resource Report Resource Website 1+ mentions |
James Cook University; Townsville; Australia (RRID:SCR_001420) | JCU | university | Public university in Townsville, Australia that functions as a research and teaching institution. Some well-known divisions of the university include the division of Tropical Environments and Societies, Tropical Health and Medicine, and Research and Innovation. | public, university, teaching, research, tropical health, environment, medicine | is parent organization of: Australian ResearCH Enabling enviRonment | Free, Freely Available | ISNI:0000 0004 0474 1797, nlx_62328, Wikidata:Q536512, Crossref funder ID:501100008451, grid.1011.1 | https://ror.org/04gsp2c11 | SCR_001420 | James Cook University | 2026-02-07 02:05:37 | 5 | ||||||
|
Computer Integrated Systems for Microscopy and Manipulation Resource Report Resource Website 1+ mentions |
Computer Integrated Systems for Microscopy and Manipulation (RRID:SCR_001413) | CISMM | training resource | Biomedical technology research center that develops force technologies applicable over a wide range of biological settings, from the single molecule to the tissue, with integrated systems that orchestrate facile instrument control, multimodal imaging, and analysis through visualization and modeling. The Force Microscope Technologies Core designs instruments in an area of science where there are unusual opportunities: the measurement of forces and the integration with optical microscopy. Force technologies play the obvious role of both measuring events in the sample and modifying the sample during the experiment. It is through the microscope that the force data is correlated with simultaneous 3D optical images. The force technology development includes the magnetic bead technology in the 3D Force Microscope project, Atomic Force Microscopy in the nanoManipulator project, and Control Software to drive the instrumentation. This core is focused on providing the physical capability to perform the experiments and probe structure/property correlations. The Ideal User Interfaces core makes the connection between the user and the instrument, the model building, and the data. This includes control systems that allow the user to move the bead inside the cell culture with a handheld pen and the visualization techniques to view the optical microscope data as a rendered 3D image collocated with the force data. Using data to create, change, and understand a model is the focus of the Advanced Model Fitting and Analysis core. The quantitative reduction of images to structural, shape, and velocity parameters is the goal of Image Analysis. The immediate understanding of correlations across image fields and between data sets in the challenge of Visualization. The power of combining the strength of a computer science graphics group with a microscopy technology group is most evident in the Graphics Hardware Acceleration project, which seeks to harness the speed of graphics processors for microscope data analysis and simulation. The Advanced Technology core pushes the boundaries of the Human Computer Interface through the investigation of improved techniques for the interaction of users with virtual environments, the real time lighting of virtual settings, and the enabling of multi-person collaboration. These techniques are validated and evaluated through physiological measures in virtual environments effectiveness evaluation studies. | microscope, visual analytics, image analysis, biomedical, bioinstrumatics, scanning electron microscope, light microscope, microscopy | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | Thrombosis, Lung disease, Cancer | NIBIB 5-P41-EB002025 | Freely Available | nlx_152648 | http://cismm.cs.unc.edu/ | SCR_001413 | UNC Chapel Hill Computer Integrated Systems for Microscopy and Manipulation | 2026-02-07 02:05:32 | 8 | ||||
|
Center for Biomedical OCT Research Resource Report Resource Website 1+ mentions |
Center for Biomedical OCT Research (RRID:SCR_001418) | CBORT | training resource | Biomedical technology research center that pioneers and provides access to microscopic imaging instruments for biologic and clinical research. Optical coherence tomography (OCT) has evolved over the last two decades to become a standard of care for diagnostic ophthalmic imaging and is poised to make significant impact in the fields of cardiology and gastrointestinal endoscopy. Access to state-of-the-art instrumentation, however, has been limited to a relatively few research laboratories and the optimization of instruments for new biomedical applications has hindered the investigation of new opportunities. A major focus of CBORT will be to cultivate strategic research collaborations and respond to a pressing need for application-specific OCT instrumentation and hardware. | imaging, optical coherence tomography, microscope, catheter, endoscopy, near infrared fluorescence | has parent organization: Harvard Medical School; Massachusetts; USA | NIBIB P41EB015903 | Free, Freely Available | nlx_152640 | SCR_001418 | Center for Biomedical OCT Research and Translation | 2026-02-07 02:05:32 | 2 | ||||||
|
BioMEMS Resource Center Resource Report Resource Website 1+ mentions |
BioMEMS Resource Center (RRID:SCR_001417) | BMRC | training resource | Biomedical technology research center that provides biomedical investigators with novel microsystems engineering tools for biological discovery, diagnostic, prognostic, and therapeutic applications. Thrust areas of interest are the development of novel living cell-based, lab-on-a-chip type devices for sorting blood cells, for high-throughput biochemistry in small volumes, and for studying cellular behavior in controlled microenvironments. | cell, tissue, microengineering, diagnostics, chip | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | NIBIB 5P41EB002503-12 | Free, Freely Available | nlx_152639 | SCR_001417 | Bio MicroElectroMechanical Systems (BioMEMS) Resource Center, Biomicroelectromechanical Systems (BioMEMS) Resource Center, BioMEMS, Bio MicroElectroMechanical Systems Resource Center | 2026-02-07 02:05:31 | 4 | ||||||
|
CisGenome Resource Report Resource Website 50+ mentions |
CisGenome (RRID:SCR_001558) | data analysis tool | Integrated software tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis. | sequencing software, chip seq, downstream analysis, chip analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian works with: TileMap |
PMID:18978777 | Free, Available for download, Freely available | OMICS_00423, biotools:cisgenome | https://bio.tools/cisgenome | http://biogibbs.stanford.edu/~jihk/CisGenome/index.htm | SCR_001558 | CisGenome v2.0 | 2026-02-07 02:05:39 | 81 |
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.
