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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 | |||||||||
|
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 | ||||||
|
flowMap Resource Report Resource Website 1+ mentions |
flowMap (RRID:SCR_002269) | software resource | Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process. | software package, mac os x, unix/linux, windows, r, flow cytometry, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_05600 | SCR_002269 | flowMap - A probabilistic algorithm for matching and comparing multiple flow cytometry samples | 2026-09-05 06:24:46 | 5 | ||||||||
|
shinyTANDEM Resource Report Resource Website |
shinyTANDEM (RRID:SCR_002169) | software resource | Software package that provides a GUI interface for rTANDEM, an R/Bioconductor package for MS/MS protein identification. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it will also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files. | mac os x, unix/linux, windows, r, mass spectrometry, proteomics |
uses: rTANDEM is listed by: OMICtools has parent organization: Bioconductor |
PMID:24700319 | Free, Available for download, Freely available | OMICS_03517 | http://www.bioconductor.org/packages/release/bioc/html/shinyTANDEM.html | http://www.bioconductor.org/packages/devel/bioc/html/shinyTANDEM.html, Resource:rTANDEM | SCR_002169 | 2026-09-05 06:24:44 | 0 | ||||||
|
flowMatch Resource Report Resource Website 1+ mentions |
flowMatch (RRID:SCR_002283) | software resource | Software for matching cell populations and building meta-clusters and templates from a collection of flow cytometry (FC) samples. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22536861 | Free, Available for download, Freely available | OMICS_05602 | SCR_002283 | flowMatch - Matching and meta-clustering in flow cytometry | 2026-09-05 06:24:46 | 1 | |||||||
|
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 | 2026-09-05 06:24:46 | 7 | |||||||
|
RankAggreg Resource Report Resource Website 10+ mentions |
RankAggreg (RRID:SCR_002225) | software resource | Software package that performs aggregation of ordered lists based on the ranks using several different algorithms: Borda count, Cross-Entropy Monte Carlo algorithm, Genetic algorithm, and a brute force algorithm. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:19228411 | GNU Lesser General Public License, v2, v2.1, v3 | OMICS_03526 | SCR_002225 | RankAggreg: Weighted rank aggregation | 2026-09-05 06:24:45 | 48 | |||||||
|
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 | 2026-09-05 06:24:45 | 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 | 2026-09-05 06:24:45 | 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 | 2026-09-05 06:24:47 | 130 | |||||||
|
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 | 2026-09-05 06:24:48 | 4 | |||||
|
Iterative Signature Algorithm Resource Report Resource Website |
Iterative Signature Algorithm (RRID:SCR_002327) | isa2, ISA | software resource | A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix. | standalone software, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:12689096 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 | biotools:isa, OMICS_03487 | https://bio.tools/isa | SCR_002327 | isa2: The Iterative Signature Algorithm | 2026-09-05 06:24:47 | 0 | |||||
|
ExomeDepth Resource Report Resource Website 100+ mentions |
ExomeDepth (RRID:SCR_002663) | software resource | Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. | software package, unix/linux, mac os x, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:22942019 | Free, Available for download, Freely available | OMICS_05443, biotools:exomedepth | https://bio.tools/exomedepth | SCR_002663 | 2026-09-05 06:24:51 | 295 | |||||||
|
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 | 2026-09-05 06:24:51 | 68 | ||||||
|
R-package for adaptive DWI analysis Resource Report Resource Website |
R-package for adaptive DWI analysis (RRID:SCR_002528) | R-package for adaptive DWI analysis | data processing software, image processing software, software application, software resource | The package dti provides methods for structural adaptive smoothing of diffusion weighted data in the context of the diffusion tensor model. Through its edge preserving properties they reduce data noise without compromizing significant structures. | afni brik, analyze, console (text based), dicom, fortran, macos, microsoft, magnetic resonance, nifti, posix/unix-like, r, diffusion weighted, dti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
Free | nlx_155934 | SCR_002528 | 2026-09-05 06:24:49 | 0 | ||||||||
|
FisHiCal Resource Report Resource Website |
FisHiCal (RRID:SCR_002799) | software resource | Software that integrates Hi-C and FISH data, offering a modular and easy-to-use tool for chromosomal spatial analysis. | standalone software, software package, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:25061071 | Free, Freely available, Available for download | OMICS_05207 | SCR_002799 | FisHiCal: Iterative FISH-based Calibration of Hi-C Data | 2026-09-05 06:24:54 | 0 | |||||||
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NetPathMiner Resource Report Resource Website 1+ mentions |
NetPathMiner (RRID:SCR_002757) | software resource | Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths. | software package, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25075120 | Free, Freely available, Available for download | biotools:netpathminer, OMICS_05210 | https://bio.tools/netpathminer | SCR_002757 | NetPathMiner: R package for network path mining through gene expression | 2026-09-05 06:24:53 | 3 | ||||||
|
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 | ||||||
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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 |
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