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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-09-12 12:55:39 | 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 | 2026-09-12 12:55:44 | 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 | 2026-09-12 12:55:44 | 68 | ||||||
|
MetaDE Resource Report Resource Website 1+ mentions |
MetaDE (RRID:SCR_000199) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:22863766 | Free, Available for download, Freely available | OMICS_04033 | http://cran.r-project.org/web/packages/MetaDE/ | SCR_000199 | MetaDE: Microarray meta-analysis for differentially expressed gene detection | 2026-09-12 12:55:04 | 1 | ||||||
|
Flicker Resource Report Resource Website |
Flicker (RRID:SCR_000288) | software resource | An open-source stand-alone computer program for visually comparing 2D gel images. | 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: SourceForge |
PMID:10027264 | Free, Available for download, Freely available | OMICS_02538, biotools:nci_flicker | https://bio.tools/nci_flicker | SCR_000288 | 2026-09-12 12:55:06 | 0 | |||||||
|
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 | |||||||
|
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 | |||||||
|
bamova Resource Report Resource Website |
bamova (RRID:SCR_000510) | bamova | data analysis software, data processing software, software application, software resource | Software that implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data). | mac os x, high throughput sequence |
is listed by: OMICtools has parent organization: University of Wyoming; Wyoming; USA |
NSF 701757 | PMID:21212231 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01532 | SCR_000510 | 2026-09-12 12:55:10 | 0 | ||||||
|
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 | ||||||||
|
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 | ||||||||
|
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 | |||||||
|
PRIDE Converter 2 Resource Report Resource Website 1+ mentions |
PRIDE Converter 2 (RRID:SCR_012051) | software resource | Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra. | standalone software, mac os x, unix/linux, windows, java, xml, mass spectrometry, pride, ols, proteomics, psi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Google Code |
PMID:22949509 | Apache License, v2 | biotools:pride_converter, OMICS_03344 | https://bio.tools/pride_converter | SCR_012051 | PRIDE, PRoteomics IDEntification (PRIDE) Converter 2 | 2026-09-12 12:57:44 | 1 | ||||||
|
jmzReader Resource Report Resource Website 1+ mentions |
jmzReader (RRID:SCR_012050) | software resource | A collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML. | standalone software, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: Google Code |
PMID:22539430 | Apache License | OMICS_03341 | SCR_012050 | 2026-09-12 12:57:44 | 2 | ||||||||
|
FIGG Resource Report Resource Website 1+ mentions |
FIGG (RRID:SCR_012064) | software resource | A large-scale whole genome simulation tool which generates large numbers of whole genomes with known sequence characteristics based on direct sampling of experimentally known or theorized variations. | standalone software, unix/linux, mac os x, windows, java, mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24885193 | Free, Public | OMICS_04164 | SCR_012064 | Frequency-based Insilico Genome Generator | 2026-09-12 12:57:44 | 3 | |||||||
|
MrBayes Resource Report Resource Website 10000+ mentions |
MrBayes (RRID:SCR_012067) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. | applet, mac os x, unix/linux, windows |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:22357727 DOI:10.1093/sysbio/sys029 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04237 | https://sources.debian.org/src/mrbayes/ | SCR_012067 | 2026-09-12 12:57:44 | 10714 |
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