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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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pracma Resource Report Resource Website 1+ mentions |
pracma (RRID:SCR_026021) | software resource, software toolkit | Software R package provides functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting. | R, numerical analysis functions, linear algebra functions, numerical optimization, differential equations, time series, | Free, Available for download, Freely available | SCR_026021 | Practical Numerical Math Functions, pracma: Practical Numerical Math Functions | 2026-09-05 06:35:11 | 9 | ||||||||||
|
University of Michigan ISR-VR Lab Core Facility Resource Report Resource Website |
University of Michigan ISR-VR Lab Core Facility (RRID:SCR_027421) | access service resource, core facility, service resource | Core provides flexible systems with built-in support for biometric data collection, dyadic interactions, and reproducible protocols. Provides access to pipelines that support reproducibility, custom data annotation, and seamless handoff to analysis tools in R, Python, and more. Provides access to IRB-ready templates and documentation, along with tested participant safety protocols and secure data management systems. | ABRF, access to IRB-ready templates and documentation, biometric data collection, dyadic interactions, reproducible protocols, custom data annotation, analysis tools, R, Python |
is listed by: ABRF CoreMarketplace has parent organization: University of Michigan; Ann Arbor; USA |
ABRF_5115 | https://coremarketplace.org/RRID:SCR_027421/?citation=1 | SCR_027421 | 2026-09-05 06:35:47 | 0 | |||||||||
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RCy3 Resource Report Resource Website 1+ mentions |
RCy3 (RRID:SCR_027668) | software resource, software toolkit, source code | Software R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort.Network biology using Cytoscape from within R. | Network biology using Cytoscape from within R, network biology, Cytoscape, R | works with: Cytoscape | Google Summer of Code ; NIGMS P41GM103504 |
PMID:31819800 | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/RCy3.html, https://zenodo.org/records/3473421 | SCR_027668 | RCy3: Network biology using Cytoscape from within R | 2026-09-05 06:35:55 | 9 | ||||||
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CYCLE Resource Report Resource Website 1+ mentions |
CYCLE (RRID:SCR_001328) | CYCLE | software resource | Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models. | r, microarray, time course, periodic expression pattern, time-series, 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:18310054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02010, biotools:cycle | http://www.bioconductor.org/packages/release/bioc/html/cycle.html, https://bio.tools/cycle | SCR_001328 | 2026-09-05 06:24:33 | 4 | ||||||
|
affylmGUI Resource Report Resource Website 10+ mentions |
affylmGUI (RRID:SCR_001320) | affylmGUI | software resource | R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11. | affymetrix, differential expression, r, data import, differential expression, gui, microarray, multiple comparison, one channel, preprocessing, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Walter and Eliza Hall Institute of Medical Research; Victoria; Australia has parent organization: Bioconductor |
PMID:16455752 | Free, Available for download, Freely available | biotools:affylmgui, OMICS_02016 | http://www.bioconductor.org/packages/release/bioc/html/affylmGUI.html, https://bio.tools/affylmgui | SCR_001320 | Affymetrix linear modeling Graphical User Interface | 2026-09-05 06:24:33 | 31 | |||||
|
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 | 2026-09-05 06:24:36 | 6 | ||||||
|
Neural Cipher Resource Report Resource Website |
Neural Cipher (RRID:SCR_001577) | Neural Cipher | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 application that interfaces with the Neural Maestro class library to perform Classical and Bayesian logistic polynomial regression analysis for multiple trial and experimental neuroscience / electrophysiological datasets. The idea is to build a neural feature extractor to plug into a neural recognition network based on recordings from patch clamps and/or brain computer interfaces. Frequency based feature sets are collected from the simulation of neuronal cell assemblies and examined for inclusion in combinatorial regressions using the Neural Maestro API. Regressions are evaluated based on different metrics. The application interfaces with a R and MATLAB API and produces a compendium to be published on CRAN. | polynomial regression analysis, neuroscience, electrophysiology, recording, patch clamp, brain computer interface, r, matlab, eeg, neuron, classical, bayesian, logistic, multiple trial, experiment |
is related to: Neural Maestro is related to: EEG time series Data Sets is related to: Rodrigo Quian Quiroga EEG ERP and single cell recordings database has parent organization: The Cromwell Workshop |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153815 | SCR_001577 | 2026-09-05 06:24:36 | 0 | ||||||||
|
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 | flowFP - Fingerprinting for Flow Cytometry | 2026-09-05 06:24:35 | 4 | |||||||
|
MCMC.qpcr Resource Report Resource Website 10+ mentions |
MCMC.qpcr (RRID:SCR_001721) | software resource | Software package that implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a classic model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:23977043 | Free, Available for download, Freely available | OMICS_03934 | SCR_001721 | MCMC.qpcr: Bayesian analysis of qRT-PCR data | 2026-09-05 06:24:38 | 24 | |||||||
|
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 | plateCore - Statistical tools and data structures for plate-based flow cytometry | 2026-09-05 06:24:38 | 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 | SLqPCR - Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH | 2026-09-05 06:24:37 | 25 | ||||||||
|
SAMstrt Resource Report Resource Website 10+ mentions |
SAMstrt (RRID:SCR_001780) | SAMstrt | software resource | Software package that provides the significance analysis of sequencing data with spike-in normalization. The statistical backgrounds and the benefits depend on SAMseq of the samr package. | differential expression, r |
is listed by: OMICtools has parent organization: Karolinska Institute; Stockholm; Sweden |
Karolinska Institutet ; Strategic Research Area Grant for Diabetes |
PMID:23995393 | Free, Available for download, Freely available | OMICS_01951 | SCR_001780 | 2026-09-05 06:24:39 | 18 | ||||||
|
NASTIseq Resource Report Resource Website 1+ mentions |
NASTIseq (RRID:SCR_001797) | NASTIseq | software resource | Software for integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. | r, antisense transcript, rna, antisense, transcript, linux, windows, strand-specific rna sequencing, cis-natural antisense transcript |
is listed by: OMICtools has parent organization: Duke University; North Carolina; USA |
PMID:23816784 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01945 | SCR_001797 | 2026-09-05 06:24:39 | 1 | |||||||
|
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 | OrderedList - Similarities of Ordered Gene Lists | 2026-09-05 06:24:40 | 11 | ||||||
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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 | flowClust - Clustering for Flow Cytometry | 2026-09-05 06:24:39 | 15 | |||||||
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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 | Combinatorial Polyfunctionality Analysis of Single Cells, COMPASS - Combinatorial Polyfunctionality Analysis of Single Cells, COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells | 2026-09-05 06:24:39 | 2 | |||||||
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TCW Resource Report Resource Website 1+ mentions |
TCW (RRID:SCR_001875) | TCW | software resource | Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R. | transcript, assembly annotation, differential expression, transcript set, ortholog, expression, linux, java, mysql, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Arizona; Arizona; USA |
NSF IOS-1044821 | PMID:23874959 | Free, Available for download, Freely available | OMICS_01940, biotools:tCW | https://bio.tools/TCW | SCR_001875 | Transcriptome Computational Workbench, TCW: Transcriptome Computational Workbench | 2026-09-05 06:24:40 | 2 | ||||
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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 | flowUtils - Utilities for flow cytometry | 2026-09-05 06:24:41 | 7 | ||||||||
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flowTrans Resource Report Resource Website 1+ mentions |
flowTrans (RRID:SCR_002093) | software resource | Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21050468 | Free, Available for download, Freely available | OMICS_05612 | SCR_002093 | flowTrans - Parameter Optimization for Flow Cytometry Data Transformation | 2026-09-05 06:24:44 | 5 | |||||||
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SNAP - SNP Annotation and Proxy Search Resource Report Resource Website 100+ mentions |
SNAP - SNP Annotation and Proxy Search (RRID:SCR_002127) | SNAP | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots | gene, genetic, genomic, r, oracle, single nucleotide polymorphism, linkage disequilibrium, genotypeing array, physical distance, membership, proxy, plot |
is listed by: OMICtools is listed by: Genetic Analysis Software is related to: International HapMap Project is related to: 1000 Genomes: A Deep Catalog of Human Genetic Variation has parent organization: Broad Institute |
NHLBI N01-HC-65226 | PMID:18974171 | Free, Freely Available | OMICS_01927, nlx_154638 | http://www.broad.mit.edu/mpg/snap/ | SCR_002127 | SNAP (SNP Annotation and Proxy Search), SNAP 2, SNP Annotation and Proxy Search | 2026-09-05 06:24:44 | 146 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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