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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
flowMeans Resource Report Resource Website 1+ mentions |
flowMeans (RRID:SCR_002275) | software resource | Software that identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. | software package, mac os x, unix/linux, windows, r, cell biology, clustering, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor is a plug in for: FlowJo |
PMID:21182178 | Artistic License, v2 | OMICS_05603 | SCR_002275 | flowMeans: Non-parametric Flow Cytometry Data Gating, flowMeans - Non-parametric Flow Cytometry Data Gating | 2026-08-01 12:02:09 | 6 | |||||||
|
flowMerge Resource Report Resource Website 1+ mentions |
flowMerge (RRID:SCR_002224) | software resource | Software for merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20049161 | Free, Available for download, Freely available | OMICS_05605 | SCR_002224 | flowMerge - Cluster Merging for Flow Cytometry Data | 2026-08-01 12:02:08 | 2 | |||||||
|
flowPhyto Resource Report Resource Website |
flowPhyto (RRID:SCR_002183) | software resource | An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data. | software package, mac os x, unix/linux, windows, r, classification, clustering, data import, flow cytometry, quality control, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21208987 | Free, Available for download, Freely available | OMICS_05606 | http://www.bioconductor.org/packages/release/bioc/html/flowPhyto.html | SCR_002183 | flowPhyto - Methods for Continuous Flow Cytometry | 2026-08-01 12:01:43 | 0 | ||||||
|
BEAT Resource Report Resource Website 100+ mentions |
BEAT (RRID:SCR_002387) | software resource | Software that implements all bioinformatics steps required for the quantitative, high-resolution analysis of DNA methylation patterns from bisulfite sequencing data. | standalone software, unix/linux, mac os x, windows, r, dna methylation, epigenetics, genetics, methyl-seq |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24618468 | GNU Lesser General Public License, v3 or greater | OMICS_03425 | SCR_002387 | BS-Seq Epimutation Analysis Toolkit, BEAT - BS-Seq Epimutation Analysis Toolkit | 2026-08-01 12:01:47 | 126 | |||||||
|
CAMERA - Collection of annotation related methods for mass spectrometry data Resource Report Resource Website 1+ mentions |
CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) | CAMERA | software resource | A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. | standalone software, mac os x, unix/linux, windows, r, spectra, extraction, annotation, liquid chromatography, mass spectrometry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:22111785 | Free, Available for download, Freely available | biotools:camera, OMICS_03366 | https://bio.tools/camera | SCR_002466 | CAMERA - Collection of annotation related methods for mass spectrometry data | 2026-08-01 12:02:10 | 4 | |||||
|
seqbias Resource Report Resource Website 10+ mentions |
seqbias (RRID:SCR_006832) | seqbias | software resource | Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
GNU Lesser General Public License | OMICS_01237, biotools:seqbias, BioTools:seqbias | https://bio.tools/seqbias, https://bio.tools/seqbias, https://bio.tools/seqbias | SCR_006832 | seqbias - Estimation of per-position bias in high-throughput sequencing data | 2026-08-01 12:03:13 | 30 | ||||||
|
MethylAid Resource Report Resource Website 50+ mentions |
MethylAid (RRID:SCR_002659) | software resource | Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored. | software package, illumina, mac os x, unix/linux, windows, r, dna methylation, gui, methylation array, microarray, quality control, two channel, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:25147358 | Free, Available for download, Freely available | biotools:methylaid, OMICS_05457 | http://www.bioconductor.org/packages/release/bioc/html/MethylAid.html, http://shiny.bioexp.nl/MethylAid/, https://bio.tools/methylaid | SCR_002659 | MethylAid - Visual and interactive quality control of large Illumina 450k data sets, MethylAid: Visual and interactive quality control of large Illumina 450k data sets | 2026-08-01 12:01:52 | 65 | ||||||
|
CGHnormaliter Resource Report Resource Website 1+ mentions |
CGHnormaliter (RRID:SCR_002936) | software resource | Software for normalization and centralization of array comparative genomic hybridization (aCGH) data with imbalanced aberrations. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). | standalone software, mac os x, unix/linux, windows, r, array comparative genomic hybridization, copy number alteration, microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20418341 | Free, Available for download, Freely available | OMICS_02572 | http://www.bioconductor.org/packages/release/bioc/html/CGHnormaliter.html | SCR_002936 | CGHnormaliter - Normalization of array CGH data with imbalanced aberrations. | 2026-08-01 12:02:15 | 2 | ||||||
|
Chimera Resource Report Resource Website 100+ mentions |
Chimera (RRID:SCR_002959) | software resource | A Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools. The current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, tophat-fusion-post and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools. | software package, unix/linux, mac os x, windows, r, infrastructure |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
PMID:25286921 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_06335 | SCR_002959 | chimera - A package for secondary analysis of fusion products | 2026-08-01 12:01:59 | 377 | |||||||
|
Triplex Resource Report Resource Website 10+ mentions |
Triplex (RRID:SCR_003061) | software resource | Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D. | software package, mac os x, unix/linux, windows, r, gene regulation, sequence matching, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23709494 | Free, Available for download, Freely available | OMICS_06259, biotools:triplex | http://www.fi.muni.cz/~lexa/triplex/, https://bio.tools/triplex | SCR_003061 | triplex - Search and visualize intramolecular triplex-forming sequences in DNA | 2026-08-01 12:02:25 | 10 | ||||||
|
rbsurv Resource Report Resource Website 1+ mentions |
rbsurv (RRID:SCR_001175) | rbsurv | software resource | Software package that selects genes associated with survival. | microarray, gene, survival, 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:rbsurv, BioTools:rbsurv, OMICS_02088 | https://bio.tools/rbsurv, https://bio.tools/rbsurv, https://bio.tools/rbsurv | SCR_001175 | rbsurv - Robust likelihood-based survival modeling with microarray data | 2026-08-01 12:01:24 | 1 | ||||||
|
ARRmNormalization Resource Report Resource Website |
ARRmNormalization (RRID:SCR_001292) | ARRmNormalization | software resource | Software package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay. | dna methylation, microarray, preprocessing, two channel, illumina |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02044 | SCR_001292 | ARRmNormalization - Adaptive Robust Regression normalization for Illumina methylation data | 2026-08-01 12:01:27 | 0 | |||||||
|
methylMnM Resource Report Resource Website 1+ mentions |
methylMnM (RRID:SCR_001289) | methylMnM | software resource | Software package to detect different methylation levels (DMR) that gives the exact p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison. | dna methylation, sequencing, medip-seq, mre-seq |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v3 | OMICS_02047 | SCR_001289 | methylMnM - detect different methylation level (DMR) | 2026-08-01 12:01:27 | 9 | |||||||
|
MergeMaid Resource Report Resource Website 1+ mentions |
MergeMaid (RRID:SCR_001221) | MergeMaid | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. R extension whose functions are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be "list", "matrix", or "ExpressionSet". The main function is "mergeExprs" which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function "intcor" calculate the correlation coefficients. Other functions use the output from "modelOutcome" to graphically display the results and cross-validate associations of gene expression data with survival. | differential expression, microarray, visualization, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16646808 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02124 | SCR_001221 | Merge Maid | 2026-08-01 12:01:35 | 3 | ||||||
|
iterativeBMAsurv Resource Report Resource Website |
iterativeBMAsurv (RRID:SCR_001254) | iterativeBMAsurv | software resource | Software package providing a variable selection method for applying survival analysis to microarray data. | microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19245714 | GNU General Public License, v2 or newer | OMICS_02086 | SCR_001254 | The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis, iterativeBMAsurv - The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis | 2026-08-01 12:01:26 | 0 | ||||||
|
snpStats: SnpMatrix and XSnpMatrix classes and methods Resource Report Resource Website 50+ mentions |
snpStats: SnpMatrix and XSnpMatrix classes and methods (RRID:SCR_001249) | snpStats | software resource | Software for classes and statistical methods for large single nucleotide polymorphism (SNP) association studies. | r, single nucleotide polymorphism, genetic variability, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:16720584 | Free, Available for download, Freely available | OMICS_02091 | SCR_001249 | 2026-08-01 12:01:44 | 78 | |||||||
|
exomeCopy Resource Report Resource Website 10+ mentions |
exomeCopy (RRID:SCR_001276) | exomeCopy | software resource | Software package for detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count. | copy number variation, genetics, sequencing, exome |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23089826 | Free, Available for download, Freely available | OMICS_02062 | http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html | SCR_001276 | exomeCopy - Copy number variant detection from exome sequencing read depth | 2026-08-01 12:01:26 | 15 | |||||
|
SMAP Resource Report Resource Website 100+ mentions |
SMAP (RRID:SCR_001270) | SMAP | software resource | Software package providing functions and classes for DNA copy number profiling of array-CGH data. | copy number variation, microarray, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18204059 | Free, Available for download, Freely available | OMICS_02068 | SCR_001270 | SMAP - A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling | 2026-08-01 12:01:26 | 199 | ||||||
|
wateRmelon Resource Report Resource Website 100+ mentions |
wateRmelon (RRID:SCR_001296) | wateRmelon | software resource | Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages. | dna methylation, microarray, 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:23631413 | Free, Available for download, Freely available | OMICS_02039, biotools:watermelon | https://bio.tools/watermelon | SCR_001296 | 2026-08-01 12:01:46 | 296 | ||||||
|
oneChannelGUI Resource Report Resource Website 10+ mentions |
oneChannelGUI (RRID:SCR_001325) | oneChannelGUI | software resource | Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. | differential expression, gui, microarray, multiple comparison, preprocessing, quality control, rna-seq, exon, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:17875544 | Free, Available for download, Freely available | biotools:onechannelgu, OMICS_02004 | http://www.bioconductor.org/packages/release/bioc/html/oneChannelGUI.html | SCR_001325 | 2026-08-01 12:01:27 | 13 |
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.
