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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FARMS Resource Report Resource Website 10+ mentions |
FARMS (RRID:SCR_001344) | FARMS | software resource | Software using a model-based technique for summarizing high-density oligonucleotide array data at probe level for Affymetrix GeneChips. It is based on a factor analysis model for which a Bayesian maximum a posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise. | oligonucleotide array, probe, affymetrix genechip, r, unix, windows, microarray, summarization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johannes Kepler University of Linz; Linz; Austria |
PMID:16473874 | Free, Freely Available | OMICS_01995, biotools:farms | https://bio.tools/farms | SCR_001344 | Factor Analysis for Robust Microarray Summarization | 2026-09-05 06:24:33 | 28 | |||||
|
CytoSPADE Resource Report Resource Website 1+ mentions |
CytoSPADE (RRID:SCR_001457) | software resource | Cytoscape plugin that provides a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm for tree-based analysis and visualization of high-dimensional cytometry data. | plugin, mac os x, unix/linux, windows, c++, java, r |
uses: Cytoscape is listed by: OMICtools has parent organization: Stanford University; Stanford; California is a plug in for: Cytoscape |
PMID:22782546 | Free, Available for download, Freely available | OMICS_05644 | http://cytospade.org/ | SCR_001457 | CytoSPADE: Cytoscape-driven Spanning tree Progression of Density normalized Events, CytoSPADE Cytoscape Plugin for SPADE, Cytoscape-driven Spanning tree Progression of Density normalized Events | 2026-09-05 06:24:34 | 2 | ||||||
|
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 | ||||||
|
InterMine Resource Report Resource Website 10+ mentions |
InterMine (RRID:SCR_001772) | software resource | An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data. | mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust | PMID:24753429 | Free, Freely available | OMICS_03840, biotools:intermine | https://github.com/intermine/intermine, https://bio.tools/intermine | http://intermine.github.io/intermine.org/ | SCR_001772 | 2026-09-05 06:24:39 | 25 | |||||
|
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 | |||||||
|
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 | |||||
|
TRAMS Resource Report Resource Website 1+ mentions |
TRAMS (RRID:SCR_002003) | TRAMS | software resource | A software program for functional annotation of genomic single nucleotide polymorphisms (SNPs) which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. It needs only a tab delimited text file containing SNP locations, reference nucleotide and SNPs in different strains along with a reference genome sequence in standard GenBank or EMBL format. It annotates SNPs as synonymous, non-synonymous or nonsense. Non-synonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms (MNPs) within a codon are combined prior to annotation. A workflow has also been developed for use in Galaxy to map short reads to a reference genome and extract and annotate the SNPs. | single nucleotide polymorphism, windows, python, mac os, linux, synonymous, non-synonymous, nonsense, annotate, genomic variation |
is listed by: OMICtools is related to: Galaxy has parent organization: FigShare |
PMID:23828175 | Free, Available for download, Freely available | OMICS_01924 | SCR_002003 | Tool for Rapid Annotation of Microbial SNPs, Tool for rapid annotation of microbial SNPs: a simple program for rapid annotation of genomic variation in prokaryotes, Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes, TRAMS: a simple program for rapid annotation of genomic variation in prokaryotes | 2026-09-05 06:24:42 | 1 | ||||||
|
Vennt Resource Report Resource Website 1+ mentions |
Vennt (RRID:SCR_002083) | software resource | A web-tool to generate dynamic Venn diagrams for differential gene expression. | unix/linux, mac os x, windows, python | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_03549 | https://github.com/drpowell/vennt | SCR_002083 | Vennt - Dynamic Venn diagrams for Differential Gene Expression | 2026-09-05 06:24:43 | 7 | |||||||
|
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 | |||||||
|
VoxBo Resource Report Resource Website 10+ mentions |
VoxBo (RRID:SCR_002166) | VoxBo | data processing software, image analysis software, image processing software, software application, software resource | Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more. | fmri, neuroimaging, brain, functional, statistical, volume, preprocessing, analysis, display, format conversion, linear, three dimensional display, workflow, lesion, analyze, c++, console (text based), dicom, image display, linux, macos, microsoft, magnetic resonance, nifti, no input/output (daemon), overlap metrics, posix/unix-like, quantification, regression, resampling, sinc function interpolation, spatial transformation, statistical operation, visualization, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: Debian has parent organization: neurodebian |
NIDA R01DA014418; NIMH R01MH073529 |
PMID:22348882 | Free, Available for download, Freely available | nif-0000-00353 | https://sources.debian.org/src/voxbo/, https://github.com/kimberg/voxbo | http://www.voxbo.org/ | SCR_002166 | 2026-09-05 06:24:44 | 13 | ||||
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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 | |||||||
|
Fiji Resource Report Resource Website 10000+ mentions |
Fiji (RRID:SCR_002285) | Fiji | data processing software, image processing software, software application, software resource, source code | Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences. | imaging, microscopy, windows, linux, java, mac osx, bio.tools |
uses: Fiji/ImageJ is used by: MuscleJ is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: ImageJ is related to: SynapseLocator is related to: Golddigger is related to: Analyze Spheroid Cell Invasion In 3D Matrix has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany has plug in: BioVoxxel Toolbox has plug in: imctools has plug in: Big Data Processor has plug in: Sholl Analysis has plug in: SAIBR has plug in: TWOMBLI |
PMID:22743772 | Free, Available for download, Freely available, Acknowledgement requested | SciRes_000137, biotools:Fiji | https://github.com/fiji/fiji, https://bio.tools/Fiji | SCR_002285 | Fiji is just ImageJ | 2026-09-05 06:24:46 | 40972 |
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