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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
RUVSeq Resource Report Resource Website 100+ mentions |
RUVSeq (RRID:SCR_006263) | software resource | Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. | software package, unix/linux, mac os x, windows, r, differential expression, preprocessing, rna-seq |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25150836 | Artistic License, v2 | OMICS_05652 | SCR_006263 | SciCrunch Registry | RUVSeq: Remove Unwanted Variation from RNA-Seq Data | 2026-11-07 11:56:11 | 481 | |||||||
|
IRanges Resource Report Resource Website 50+ mentions |
IRanges (RRID:SCR_006420) | IRanges | software resource | Software tool for computing and annotating genomic ranges.Provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent Vector API as much as possible. | Annotating genomic ranges, computing genomic ranges, genomic ranges, storing ranges of integers, bio.tools |
is used by: riboWaltz is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:23950696 | Free, Available for download, Freely available | OMICS_01163, biotools:iranges | https://bio.tools/iranges | SCR_006420 | SciCrunch Registry | Infrastructure for manipulating intervals on sequences | 2026-11-07 11:55:53 | 88 | |||||
|
virtualArray Resource Report Resource Website 1+ mentions |
virtualArray (RRID:SCR_001361) | virtualArray | software resource | Software package that permits the user to combine raw data of different microarray platforms into one virtual array. It consists of several functions that act subsequently in a semi-automatic way. Doing as much of the data combination and letting the user concentrate on analyzing the resulting virtual array. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Leipzig; Saxony; Germany |
PMID:23452776 | Free, Available for download, Freely available | OMICS_01979 | http://www.bioconductor.org/packages/release/bioc/html/virtualArray.html | SCR_001361 | SciCrunch Registry | 2026-11-07 11:54:23 | 5 | ||||||
|
stepNorm Resource Report Resource Website |
stepNorm (RRID:SCR_001359) | stepNorm | software resource | Software for stepwise normalization functions for cDNA microarray data. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of California at San Francisco; California; USA |
PMID:16646857 | Free, Available for download, Freely available | OMICS_01981 | SCR_001359 | SciCrunch Registry | stepNorm - Stepwise normalization functions for cDNA microarrays | 2026-11-07 11:54:29 | 0 | ||||||
|
RAMA Resource Report Resource Website 50+ mentions |
RAMA (RRID:SCR_001358) | RAMA | software resource | Software package for robust estimation of cDNA microarray intensities with replicates. It uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or newer | OMICS_01982 | SCR_001358 | SciCrunch Registry | Robust Analysis of MicroArrays | 2026-11-07 11:54:17 | 66 | |||||||
|
MANOR Resource Report Resource Website 10+ mentions |
MANOR (RRID:SCR_001305) | MANOR | software resource | Software packqge for importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH (Comparative genomic hybridization) experiments. | copy number variation, data import, microarray, preprocessing, quality control, two channel, comparative genomic hybridization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02028 | SCR_001305 | SciCrunch Registry | CGH Micro-Array NORmalization | 2026-11-07 11:54:15 | 17 | |||||||
|
dyebias Resource Report Resource Website |
dyebias (RRID:SCR_001308) | dyebias | software resource | Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias. | microarray, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:17623705 | GNU General Public License, v3 | biotools:dyebias, OMICS_02025 | https://bio.tools/dyebias | SCR_001308 | SciCrunch Registry | dyebias - The GASSCO method for correcting for slide-dependent gene-specific dye bias | 2026-11-07 11:54:21 | 0 | |||||
|
limmaGUI Resource Report Resource Website 10+ mentions |
limmaGUI (RRID:SCR_001306) | limmaGUI | software resource | Software package for a Graphical User Interface for the limma Microarray package. | differential expression, gui, microarray, multiple comparison, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:15297296 | Free, Available for download, Freely available | OMICS_02027, biotools:limmagui | https://bio.tools/limmagui | SCR_001306 | SciCrunch Registry | limmaGUI - GUI for limma package | 2026-11-07 11:54:26 | 14 | |||||
|
ffpe Resource Report Resource Website 500+ mentions |
ffpe (RRID:SCR_001307) | ffpe | software resource | Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots). | formalin-fixed, paraffin-embedded, gene expression, microarray, quality control, 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_02026, biotools:ffpe | https://bio.tools/ffpe | SCR_001307 | SciCrunch Registry | ffpe - Quality assessment and control for FFPE microarray expression data | 2026-11-07 11:54:29 | 524 | ||||||
|
asSeq Resource Report Resource Website 1+ mentions |
asSeq (RRID:SCR_001625) | asSeq | data analysis software, data processing software, software application, software resource, source code | Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq | r, rna-seq, expression quantitative trait locus, total read count, allele-specific expression, allele-specific gene expression, gene expression quantitative trait locus, rna isoform, gene expression, genetic marker, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Bioconductor has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:21838806 | Free, Available for download, Freely available | OMICS_01948, nlx_153893, biotools:asseq | https://bio.tools/asseq | SCR_001625 | SciCrunch Registry | 2026-11-07 11:54:35 | 6 | ||||||
|
ACME Resource Report Resource Website 50+ mentions |
ACME (RRID:SCR_001464) | ACME | software resource | A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. | microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: National Institutes of Health |
PMID:16939795 | Free, Available for download, Freely available | OMICS_01976 | SCR_001464 | SciCrunch Registry | Algorithms for Calculating Microarray Enrichment | 2026-11-07 11:54:30 | 62 | ||||||
|
CoGAPS Resource Report Resource Website 10+ mentions |
CoGAPS (RRID:SCR_001479) | CoGAPS | software resource | Software that infers biological processes which are active in individual gene sets from corresponding microarray measurements. It achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets. | gene expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20810601 | Free, Available for download, Freely available | OMICS_01973 | SCR_001479 | SciCrunch Registry | Coordinated Gene Activity in Pattern Sets | 2026-11-07 11:54:25 | 38 | ||||||
|
flowFP Resource Report Resource Website 1+ mentions |
flowFP (RRID:SCR_001537) | software resource | A Bioconductor software package for fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956416 | Free, Available for download, Freely available | OMICS_05599 | SCR_001537 | SciCrunch Registry | flowFP - Fingerprinting for Flow Cytometry | 2026-11-07 11:54:31 | 4 | |||||||
|
plateCore Resource Report Resource Website |
plateCore (RRID:SCR_001743) | data or information resource, database, software resource | Software that provides basic S4 data structures and routines for analyzing plate based flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956418 | Free, Available for download, Freely available | OMICS_05641 | http://www.bioconductor.org/packages/release/bioc/html/plateCore.html | SCR_001743 | SciCrunch Registry | plateCore - Statistical tools and data structures for plate-based flow cytometry | 2026-11-07 11:54:33 | 0 | ||||||
|
SLqPCR Resource Report Resource Website 10+ mentions |
SLqPCR (RRID:SCR_001669) | software resource | Software functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH. | standalone software, mac os x, unix/linux, windows, r, microtitre plate assay, qpcr |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_04010 | SCR_001669 | SciCrunch Registry | SLqPCR - Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH | 2026-11-07 11:54:29 | 25 | ||||||||
|
OrderedList Resource Report Resource Website 10+ mentions |
OrderedList (RRID:SCR_001834) | software resource | An R / bioconductor package for detecting similarity in ordered gene lists. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively. | standalone software, mac os x, unix/linux, windows, r, differential expression, microarray, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16844712 | Free, Available for download, Freely available | OMICS_03525 | http://compdiag.molgen.mpg.de/software/OrderedList.shtml | SCR_001834 | SciCrunch Registry | OrderedList - Similarities of Ordered Gene Lists | 2026-11-07 11:54:27 | 11 | ||||||
|
R Project for Statistical Computing Resource Report Resource Website 10000+ mentions |
R Project for Statistical Computing (RRID:SCR_001905) | R | software resource | Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS. | R software, statistical, computing, graphics, programming, language, bio.tools |
is used by: UTR is used by: MSstats is used by: CummeRbund is used by: deFuse is used by: JASP is used by: Boruta is used by: NMRProcFlow is used by: PlotsOfData is used by: rtransparent is used by: shinyCircoss is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: CRAN is affiliated with: factoextra is affiliated with: dendsort is affiliated with: viridis is affiliated with: RColorBrewer is affiliated with: statmod is related to: Sweave is related to: rOpenSci is related to: R Manuals is related to: Bioconductor is related to: ggplot2 is related to: madsim is related to: Solas is related to: braincog is related to: clustree is related to: PhenoSpD is related to: geomorph is related to: NeuroAnatomy Toolbox is related to: dplyr is related to: glmmADMB is related to: clusterProfiler is related to: ropls is related to: mixOmics is related to: FlowSOM is related to: Rtsne is related to: scran is related to: Rsubread is related to: riboSeqR is related to: Biostrings is related to: riboWaltz is related to: GenomicFeatures is related to: devtools is related to: affy is related to: affydata is related to: Heatmapper is related to: toxprofileR is related to: LTRpred is related to: RaceID is related to: PRSice is related to: Genomic Ranges is related to: Goseq is related to: GAGE is related to: metagear is related to: pagoda2 is related to: dndSCV is related to: tidyr is related to: ClustVis is related to: IDR is related to: NeuroAnatomy Toolbox is related to: rjags is related to: gProfiler2 is related to: knitr is related to: EpiEstim is related to: Minimum-Hypergeometric Test is related to: Network-Based R-Statistics is related to: seqpac is related to: survminer is related to: Vector Generalized Linear and Additive Models is related to: LEA is related to: StAMPP is related to: Betareg is related to: Harrell Miscellaneous is related to: simplePHENOTYPES is related to: Bayesian Generalized Linear Regression is related to: ranger is related to: h2o4gpu is related to: ridge regression Best Linear Unbiased Prediction is related to: Classification And Regression Training is related to: Rphenograph is related to: Peptides is related to: taxize is related to: seqinr is related to: reshape2 is related to: monaLisa is related to: mia is related to: Rtsne is related to: R package:stats-package is related to: R package: maxstat is related to: stats |
PMID:18252159 | SCR_021974, nif-0000-10474, OMICS_01147, biotools:r | https://cran.r-project.org/src/base/R-3/, https://bio.tools/r | SCR_001905 | SciCrunch Registry | R software, The R Project for Statistical Computing, R project, R Project, R, R version 3.5.1, R Package, R-3, R version 3.6.1, R Project for Statistical Computing | 2026-11-07 11:54:46 | 52118 | ||||||
|
flowClust Resource Report Resource Website 10+ mentions |
flowClust (RRID:SCR_001807) | software resource | A Bioconductor software package for automated gating of flow cytometry data that implements a robust model-based clustering approach based on multivariate t mixture models with the Box-Cox transformation. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19442304 | Artistic License, v2 | OMICS_05595 | SCR_001807 | SciCrunch Registry | flowClust - Clustering for Flow Cytometry | 2026-11-07 11:54:34 | 15 | |||||||
|
COMPASS Resource Report Resource Website 1+ mentions |
COMPASS (RRID:SCR_001801) | software resource | Software for combinatorial polyfunctionality analysis of single cells. It is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. It uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:26006008 | Free, Available for download, Freely available | OMICS_05640 | SCR_001801 | SciCrunch Registry | , Combinatorial Polyfunctionality Analysis of Single Cells, Combinatorial Polyfunctionality Analysis of Antigen-Specific T-cells, COMPASS - Combinatorial Polyfunctionality Analysis of Single Cells, COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells | 2026-11-07 11:54:34 | 2 | |||||||
|
flowUtils Resource Report Resource Website 1+ mentions |
flowUtils (RRID:SCR_001879) | software resource | Software that provides utilities for flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, decision tree, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05614 | SCR_001879 | SciCrunch Registry | flowUtils - Utilities for flow cytometry | 2026-11-07 11:54:35 | 7 |
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.
