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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-05 06:24:32 | 18 | |||||
|
Neural Maestro Resource Report Resource Website |
Neural Maestro (RRID:SCR_001563) | Neural Maestro | data access protocol, software application, software library, software resource, software toolkit, web service | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. A C#.NET/C++.NET 4.0 API multi-threaded, parallel class library with CUDA kernels for EEG predictive analytics gleaned from the ModelMaker 2 application. This web service and component library offers functionality to do univariate and multivariate nonlinear time series and frequency based predictive analysis for EEG / Ecog / MEG signals for gaming applications. Neural Maestro works with both EEGLab / BCILab and eConnectome as well as other MATLAB and R packages. It enables one to build highly sophisticated neuroscience applications with little effort in Windows applications. | univariate, multivariate, nonlinear time series, time series, frequency, predictive analysis, eeg, ecog, meg, gaming application, neuroscience, computer gaming, modeling, forecasting, matlab, r, artificial intelligence, analytics, neural assessment |
is related to: EEGLAB is related to: Neural Cipher is related to: BCILAB is related to: ModelMaker is related to: iBIOFind has parent organization: The Cromwell Workshop |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153440 | SCR_001563 | 2026-09-05 06:24:36 | 0 | ||||||||
|
The Cromwell Workshop Resource Report Resource Website |
The Cromwell Workshop (RRID:SCR_001588) | TCW | service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. Statistical and biomedical informatics software studio that develops neuroscience applications and brain computer interface games. They are dedicated to the integration of medical research, neuroscience, time series analysis, computer programming, statistics, sensor technologies, graphics design, artificial intelligence and entertainment to build gaming systems for neuroscientific research and intelligent tutoring in the classroom and lab. The current focus of The Cromwell Workshop/Neuronal Architects is on theoretical neuroscience and experimental modeling of psychological and neural processes that involve attention, emotion, motivation and executive functions that are impaired by neurological diseases. The outcome of this work is to use these results in the design of multiple genre brain computer interface gaming systems that can be used in both clinical and at home settings. If you would like to explore any collaborative opportunities to use their software or enhance your existing statistical products with their .NET, Java, R and Matlab code bases, let them know. | statistical software, web design, medical research, neuroscience, time series analysis, computer programming, statistics, sensor technology, graphics design, artificial intelligence, entertainment, gaming system, modeling, psychological process, neural process, attention, emotion, motivation, executive function, neurological disease, brain computer interface, .net, java, r, matlab, computational neuroscience, time series, gaming |
is parent organization of: Neural Maestro is parent organization of: Neural Cipher is parent organization of: iBIOFind is parent organization of: eNeoTutor is parent organization of: ModelMaker |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153830 | SCR_001588 | Cromwell Workshop | 2026-09-05 06:24:36 | 0 | |||||||
|
rMAT Resource Report Resource Website 10+ mentions |
rMAT (RRID:SCR_001583) | data analysis software, data processing software, software application, software resource, source code | Software package for normalizing and analyzing tiling arrays and ChIP-chip data. It is the R-version of a MAT program. | chip-seq, normalize data, tiling array, mat, r |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20089513 | Free, Available for download, Freely available | OMICS_00810 | http://www.rglab.org | SCR_001583 | 2026-09-05 06:24:36 | 16 | |||||||
|
CNVrd2 Resource Report Resource Website 1+ mentions |
CNVrd2 (RRID:SCR_001723) | software resource | A software package that uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions. | standalone software, illumina, unix/linux, mac os x, windows, r, clustering., copy number variation, coverage, linkage disequilibrium, snp, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23646200 | Free, Available for download, Freely available | OMICS_03924 | http://www.bioconductor.org/packages/release/bioc/html/CNVrd2.html, https://github.com/hoangtn/CNVrd2 | SCR_001723 | CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data | 2026-09-05 06:24:38 | 5 | ||||||
|
TaLasso Resource Report Resource Website 1+ mentions |
TaLasso (RRID:SCR_001726) | TaLasso | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool for quantification of human miRNA-mRNA Interactions. TaLasso is also available as Matlab or R code. | mirna, mrna, matlab, r, gene expression, gene |
is listed by: OMICtools has parent organization: Autonomous University of Madrid; Madrid; Spain |
PMID:22348024 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00417 | SCR_001726 | 2026-09-05 06:24:38 | 1 | |||||||
|
pairedBayes Resource Report Resource Website 1+ mentions |
pairedBayes (RRID:SCR_001738) | pairedBayes | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R code for Bayesian modeling of paired RNA-seq experiments. | r, rna-seq |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_01958 | SCR_001738 | 2026-09-05 06:24:38 | 1 | ||||||||
|
unifiedWMWqPCR Resource Report Resource Website |
unifiedWMWqPCR (RRID:SCR_001706) | software resource | Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data. | standalone software, mac os x, unix/linux, windows, r, gene expression, microtitre plate assay, qpcr, differential expression, multiple comparison, quality control, visualization, qpcr, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24794933 | Free, Available for download, Freely available | OMICS_03937, biotools:unifiedwmwqpcr | https://bio.tools/unifiedwmwqpcr | SCR_001706 | unifiedWMWqPCR - Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data | 2026-09-05 06:24:38 | 0 | ||||||
|
RSVSim Resource Report Resource Website 10+ mentions |
RSVSim (RRID:SCR_001777) | software resource | A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates. | unix/linux, mac os x, windows, r, sequencing, structural variation |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23620362 | Free, Available for download, Freely available | OMICS_03822 | SCR_001777 | RSVSim: an R/Bioconductor package for the simulation of structural variations | 2026-09-05 06:24:39 | 16 | |||||||
|
GenABEL Resource Report Resource Website 500+ mentions |
GenABEL (RRID:SCR_001842) | software library, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits. | r, genome-wide association, single nucleotide polymorphism |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: SoftCite |
Centre for Medical Systems Biology; Netherlands ; Netherlands Genomics Initiative ; Netherlands Organisation for Scientific Research ; Russian Foundation for Basic Research |
PMID:17384015 DOI:10.1186/1471-2105-11-134 DOI:10.1093/bioinformatics/btm108 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154328, OMICS_00234 | http://mga.bionet.nsc.ru/~yurii/ABEL/GenABEL/, https://cran.r-project.org/web/packages/GenABEL/index.html, https://sources.debian.org/src/probabel/ | SCR_001842 | GenABEL package, R/GENABEL | 2026-09-05 06:24:40 | 506 | |||||
|
SamSPECTRAL Resource Report Resource Website 1+ mentions |
SamSPECTRAL (RRID:SCR_001858) | software resource | Software that identifies cell population in flow cytometry data. It demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. It samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample. | software package, mac os x, unix/linux, windows, r, cell biology, clustering, flow cytometry, stem cell, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Cancer, HIV | PMID:20667133 | Free, Available for download, Freely available | OMICS_05638, biotools:samspectral | https://bio.tools/samspectral | SCR_001858 | SamSPECTRAL - Identifies cell population in flow cytometry data | 2026-09-05 06:24:40 | 4 | |||||
|
RchyOptimyx Resource Report Resource Website 1+ mentions |
RchyOptimyx (RRID:SCR_001889) | software resource | Software that constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response). | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23044634 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05637 | SCR_001889 | RchyOptimyx - Optimyzed Cellular Hierarchies for Flow Cytometry, RchyOptimyx: Optimyzed Cellular Hierarchies for Flow Cytometry | 2026-09-05 06:24:41 | 3 | |||||||
|
SPADE Resource Report Resource Website 100+ mentions |
SPADE (RRID:SCR_001810) | data analysis software, data processing software, data visualization software, software application, software resource | An analysis and visualization software tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, gui, graph, network, visualization |
is listed by: OMICtools has parent organization: Bioconductor is a plug in for: FlowJo |
PMID:21964415 | Free, Available for download, Freely available | OMICS_05639 | http://cytospade.org/ | http://www.bioconductor.org/packages/release/bioc/html/spade.html | SCR_001810 | Spanning tree Progression of Density normalized Events, SPADE - An analysis and visualization tool for Flow Cytometry | 2026-09-05 06:24:39 | 285 | |||||
|
flowType Resource Report Resource Website 1+ mentions |
flowType (RRID:SCR_001957) | software resource | Software for phenotyping Flow Cytometry assays using multidimentional expansion of single dimentional partitions. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22383736 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05613 | SCR_001957 | flowType - Phenotyping Flow Cytometry Assays | 2026-09-05 06:24:42 | 9 | |||||||
|
ADaCGH2 Resource Report Resource Website |
ADaCGH2 (RRID:SCR_001981) | software resource | Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data. | standalone software, mac os x, unix/linux, windows, r, copy number variant, microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24532724 | Free, Available for download, Freely available | biotools:adacgh2, OMICS_03697 | https://bio.tools/adacgh2 | SCR_001981 | ADaCGH2 - Analysis of big data from aCGH experiments using parallel computing and ff objects | 2026-09-05 06:24:42 | 0 | ||||||
|
PurBayes Resource Report Resource Website 10+ mentions |
PurBayes (RRID:SCR_002068) | software resource | An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data. | 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:23749958 | Free, Available for download, Freely available | biotools:purbayes, OMICS_03561 | https://bio.tools/purbayes | http://cran.r-project.org/web/packages/PurBayes/ | SCR_002068 | PurBayes: Bayesian Estimation of Tumor Purity and Clonality | 2026-09-05 06:24:43 | 11 | |||||
|
TEQC Resource Report Resource Website 10+ mentions |
TEQC (RRID:SCR_001943) | software resource | An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on. | standalone software, unix/linux, mac os x, windows, r, genetics, microarray, quality control, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21398674 | Free, Available for download, Freely available | OMICS_03602 | SCR_001943 | TEQC - Quality control for target capture experiments | 2026-09-05 06:24:42 | 14 | |||||||
|
flowViz Resource Report Resource Website 10+ mentions |
flowViz (RRID:SCR_002075) | software resource | Software that provides visualization tools for flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18245128 | Free, Available for download, Freely available | OMICS_05615 | SCR_002075 | flowViz - Visualization for flow cytometry | 2026-09-05 06:24:43 | 31 | |||||||
|
flowQB Resource Report Resource Website |
flowQB (RRID:SCR_002144) | software resource | A fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05610 | http://www.bioconductor.org/packages/release/bioc/html/flowQB.html | SCR_002144 | B and CVinstrinsic calculations, flowQB - Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, flowQB: Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q | 2026-09-05 06:24:44 | 0 | |||||||
|
flowFit Resource Report Resource Website 1+ mentions |
flowFit (RRID:SCR_002286) | software resource | A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24681909 | Artistic License, v2 | OMICS_05601 | SCR_002286 | flowFit - Estimate proliferation in cell-tracking dye studies | 2026-09-05 06:24:46 | 4 |
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