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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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cuteNMR Resource Report Resource Website |
cuteNMR (RRID:SCR_000347) | software resource | A multi-platform NMR processing application. | standalone software, mac os x, unix/linux, windows, c++ |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_03391 | SCR_000347 | 2026-09-12 12:55:07 | 0 | |||||||||
|
JMolDraw Resource Report Resource Website |
JMolDraw (RRID:SCR_000349) | software resource | 2-D chemical structure drawing software program. | applet, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_05000 | SCR_000349 | 2026-09-12 12:55:07 | 0 | |||||||||
|
flowFlowJo Resource Report Resource Website 10+ mentions |
flowFlowJo (RRID:SCR_000410) | software resource | A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956421 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05598 | SCR_000410 | flowFlowJo - Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm | 2026-09-12 12:55:08 | 21 | |||||||
|
IrfanView Resource Report Resource Website 10+ mentions |
IrfanView (RRID:SCR_000315) | software resource | An open source graphic viewer. Some features include batch conversion, paint options, basic editing and several supported file formats. It is compatible with Windows 9x, ME, NT, 2000, XP, 2003 , 2008, Vista, Windows 7, Windows 8, and Windows 10. | graphic viewer, open source, windows | Free, Available for download, Freely available | nlx_157659 | SCR_000315 | 2026-09-12 12:55:07 | 13 | ||||||||||
|
Micro-Analyzer Resource Report Resource Website |
Micro-Analyzer (RRID:SCR_000394) | Micro-Analyzer | software resource | Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems. | windows, linux, java, java swing, gene expression, snp, microarray, affymetrix, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23731720 | Free, Available for download, Freely available | OMICS_01919, biotools:microanalyzer | https://bio.tools/microanalyzer | SCR_000394 | microAnalyzer | 2026-09-12 12:55:08 | 0 | |||||
|
flowStats Resource Report Resource Website 1+ mentions |
flowStats (RRID:SCR_000399) | software resource | Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05611 | SCR_000399 | flowStats - Statistical methods for the analysis of flow cytometry data | 2026-09-12 12:55:08 | 1 | ||||||||
|
iBMQ Resource Report Resource Website |
iBMQ (RRID:SCR_000481) | software resource | Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently. | standalone software, mac os x, unix/linux, windows, r, gene expression, microarray, preprocessing, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23958729 | Free, Available for download, Freely available | OMICS_04601 | SCR_000481 | iBMQ - integrated Bayesian Modeling of eQTL data | 2026-09-12 12:55:10 | 0 | |||||||
|
Simulx Resource Report Resource Website 1+ mentions |
Simulx (RRID:SCR_000486) | Simulx | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8, 2025. R function for computing predictions and simulating data from both Mlxtran and PharmML models that is based on MlxCompute, the model simulation engine developed by Lixoft. MlxCompute combines the Mlxtran language interpreter with the equation solvers to compute efficiently complex systems of ordinary differential equations (ODEs) and delayed differential equations (DDEs). Simulx takes advantage of the modularity of hierarchical models for simulating different components of a model: models for population parameters, individual covariates, individual parameters and longitudinal data, including continuous, count, categorical, and time-to-event data. It is also extremely flexible for defining complex dose regimens. Simulx will be the core of the next version of the DDMoRe Clinical Trial Simulator. | windows, linux, macos, model, r, simulation, population, covariate, dose regimen |
is related to: PharmML has parent organization: DDMoRe has parent organization: National Institute for Research in Computer Science and Control; Brittany; France |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158166 | SCR_000486 | 2026-09-12 12:55:10 | 2 | ||||||||
|
flowQ Resource Report Resource Website |
flowQ (RRID:SCR_000575) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for 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 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05805 | SCR_000575 | flowQ: Quality control for flow cytometry | 2026-09-12 12:55:11 | 0 | ||||||||
|
SigFuge Resource Report Resource Website |
SigFuge (RRID:SCR_000444) | software resource | Algorithm for testing significance of clustering in RNA-seq data. | software package, unix/linux, mac os x, windows, r, clustering, rna-seq, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25030904 | Free, Available for download, Freely available | OMICS_05201 | SCR_000444 | 2026-09-12 12:55:09 | 0 | ||||||||
|
Distributed Computing Engine Resource Report Resource Website |
Distributed Computing Engine (RRID:SCR_000781) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. Software designed to serve as a distributed computational framework to help perform mathematical simulations of muscle contraction. DEngine has a Windows PC, central controller PC and mathematical models that run as console applications on clients. | distributed, computational, framework, math, simulation, muscle, contraction, windows, model | has parent organization: University of Kentucky; Kentucky; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30413 | SCR_000781 | DEngine | 2026-09-12 12:55:14 | 0 | ||||||||
|
jmzIdentML API Resource Report Resource Website |
jmzIdentML API (RRID:SCR_000878) | software resource | A Java application programming interface (API) for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. | standalone software, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: Google Code |
PMID:22539429 | Free, Available for download, Freely available | OMICS_03339 | SCR_000878 | 2026-09-12 12:55:15 | 0 | ||||||||
|
LONI Pipeline Processing Environment Resource Report Resource Website 10+ mentions |
LONI Pipeline Processing Environment (RRID:SCR_001161) | LONI Pipeline | data processing software, software application, software resource, workflow software | A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely. | workflow, neuroscience, afni brik, analyze, bshort, bfloat, computational neuroscience, dicom, imaging genomics, java, linux, macos, microsoft, minc, minc2, nifti, pet, spect, posix/unix-like, sunos/solaris, windows, windows nt/2000, atlas, birn, ccb, functional, na-mic, registration, segmentation, statistical, surface analysis, visual processing environment, volume, warping, image processing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR P41 RR013642; NIMH R01 MH71940; NCRR U54 RR021813 |
PMID:12880830 | Free, Available for download, Freely available | nif-0000-00322 | http://www.nitrc.org/projects/pipeline | http://www.loni.ucla.edu/NCRR/Software/Pipeline.html | SCR_001161 | LONI Pipeline Environment | 2026-09-12 12:55:20 | 11 | |||
|
flowWorkspace Resource Report Resource Website 1+ mentions |
flowWorkspace (RRID:SCR_001155) | software resource | Software package that facilitates comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis. | software package, mac os x, unix/linux, windows, r, data import, data representation, flow cytometry, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23020243 | Free, Available for download, Freely available | OMICS_05616 | SCR_001155 | flowWorkspace - Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore | 2026-09-12 12:55:20 | 3 | |||||||
|
APSampler Resource Report Resource Website |
APSampler (RRID:SCR_000042) | software resource | A software tool that allows multi-locus and multi-level association analysis of genotypic and phenotypic data. | mac os x, unix/linux, windows, c, c++, perl | has parent organization: Google Code | PMID:16118183 | Free, Available for download, Freely available | OMICS_04023 | http://code.google.com/p/apsampler/ | SCR_000042 | 2026-09-12 12:55:02 | 0 | |||||||
|
SP-Designer Resource Report Resource Website |
SP-Designer (RRID:SCR_000031) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa. | standalone software, windows |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23634845 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03932 | SCR_000031 | 2026-09-12 12:55:01 | 0 | ||||||||
|
Megraft Resource Report Resource Website |
Megraft (RRID:SCR_000240) | Megraft | software resource | A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes. | windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22824070 | Free, Available for download, Freely available | biotools:megraft, OMICS_02161 | https://bio.tools/megraft | SCR_000240 | 2026-09-12 12:55:05 | 0 | ||||||
|
Oqtans Resource Report Resource Website |
Oqtans (RRID:SCR_011905) | Oqtans | software resource | It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis. | windows, illumina | is listed by: OMICtools | Apache License | OMICS_01407 | SCR_011905 | Online Quantitative Transcriptome Analysis | 2026-09-12 12:57:42 | 0 | |||||||
|
Viewmol Resource Report Resource Website |
Viewmol (RRID:SCR_012088) | software resource | Software providing a graphical front end for computational chemistry programs. | standalone software, windows, c, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
GNU General Public License | OMICS_05057 | https://sources.debian.org/src/viewmol/ | SCR_012088 | 2026-09-12 12:57:45 | 0 | ||||||||
|
QuteMol Resource Report Resource Website 10+ mentions |
QuteMol (RRID:SCR_012089) | software resource | Open source (GPL) software providing an interactive, high quality molecular visualization system. | standalone software, unix/linux, windows |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:17080857 DOI:10.1109/TVCG.2006.115 |
Free, Freely available | OMICS_05075 | https://sources.debian.org/src/qutemol/ | SCR_012089 | 2026-09-12 12:57:45 | 14 |
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