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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AS-Peak Resource Report Resource Website 1+ mentions |
AS-Peak (RRID:SCR_000380) | ASPeak | software resource | A software that utilizes a peak detection algorithm to identify RNA-protein binding sites. | rna, peak detection, protein, binding, site, algorithm, analysis |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23929032 | Free, Available for download, Freely available | OMICS_00566 | https://omictools.com/aspeak-tool | SCR_000380 | 2026-09-05 06:24:18 | 2 | ||||||
|
GENSENG Resource Report Resource Website 1+ mentions |
GENSENG (RRID:SCR_000378) | data analysis software, data processing software, software application, software resource | Software for detecting copy number variations from next generation sequencing data. Used to identify regions of discrete copy number changes while simultaneously accounting for effects of multiple confounders. | next generation sequencing data, detecting copy number variations, discrete copy number changes, identify regions |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23275535 | Free, Available for download, Freely available | OMICS_00345 | SCR_000378 | 2026-09-05 06:24:18 | 1 | ||||||||
|
ArrayPlex Resource Report Resource Website |
ArrayPlex (RRID:SCR_000312) | ArrayPlex | software resource | Open source software that integrates various forms of microarray data from diverse annotation and primary data sources. This software provides a programmatic framework (API set) that will be used for collaborative development and deploys an easy to maintain client-server architecture. | microarray, programmatic framework, collaborative, client-server, |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19014503 | Free, Available for download, Freely available | OMICS_00745 | SCR_000312 | 2026-09-05 06:24:16 | 0 | |||||||
|
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 | 2026-09-05 06:24:18 | 0 | |||||
|
FunctSNP Resource Report Resource Website |
FunctSNP (RRID:SCR_000393) | FunctSNP | software resource | An R package for linking SNPs (Single Nucleotide Polymorphisms) to functional knowledge. | single nucleotide polymorphism |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20534127 | Free, Available for download, Freely available | OMICS_01925 | SCR_000393 | FunctSNP - Linking SNPs to functional knowledge | 2026-09-05 06:24:18 | 0 | ||||||
|
LIPAGE Resource Report Resource Website 1+ mentions |
LIPAGE (RRID:SCR_000290) | data management software, software application, software resource | Laboratory information management system for proteomics. The software works with 2DPAGE-based proteomics workflow. | proteomics, laboratory, open source, 2dpage, management system |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17018156 | Free, Available for download, Freely available | OMICS_02553 | SCR_000290 | LIMS for proteomics | 2026-09-05 06:24:17 | 1 | |||||||
|
MIGen Resource Report Resource Website 10+ mentions |
MIGen (RRID:SCR_006959) | MIGen | data or information resource, knowledge environment, narrative resource, standard specification | Standard specification for the information required to report a genotyping experiment, covering: study and experiment design, subject information, genotyping procedure, and data analysis methods. The goal is to set a reporting standard for adoption by the research community to facilitate consistent data interpretation and independent validation/reproduction, and to serve as guidance for database design for storing genotyping experiment data. MIGen is being developed as a collaborative project involving international domain experts and is a registered project under MIBBI: Minimum Information for Biological and Biomedical Investigations. | genotyping, genotype, genotyping experiment, data archiving, data management, data sharing, data transfer, data analysis, experiment |
is listed by: OMICtools is related to: Minimum Information for Biological and Biomedical Investigations has parent organization: SourceForge has parent organization: UT Southwestern Medical Center Department of Pathology |
The community can contribute to this resource | OMICS_01786 | SCR_006959 | Minimum Information about a Genotyping Experiment | 2026-09-05 06:30:00 | 20 | |||||||
|
SAM format Resource Report Resource Website 1000+ mentions |
SAM format (RRID:SCR_012093) | data or information resource, interchange format, narrative resource, standard specification | A generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19505943 | OMICS_05115 | SCR_012093 | Sequence Alignment/Map format | 2026-09-05 06:30:03 | 1274 | |||||||||
|
MaryGold Resource Report Resource Website 1+ mentions |
MaryGold (RRID:SCR_000528) | MaryGold | software resource, software toolkit | Software package that enables detection of sequence variation between metagenomic samples. | sequence variation, metagenomic, c++, python |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available, | OMICS_01495 | SCR_000528 | MaryGold - Variation analysis of metagenomic samples | 2026-09-05 06:30:35 | 1 | |||||||
|
Bioelectromagnetism Matlab Toolbox Resource Report Resource Website 1+ mentions |
Bioelectromagnetism Matlab Toolbox (RRID:SCR_006090) | data processing software, software application, software resource, software toolkit | Software toolbox to facilitate quick and easy import, visualization and measurement for Event Related Potential (ERP) data. The toolbox can open and visualise ERP averaged data (Neuroscan, ascii formats), 2D/3D electrode coordinates and 3D cerebral tissue tesselations (meshes). All the features can be explored quickly and easily using the example data provided in the toolbox. The GUI interface is simple and intuitive. | eeg, meg, mri, electrocorticography, event related potential, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ERPLAB has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
GNU General Public License | nif-0000-00268 | http://www.nitrc.org/projects/eeg | SCR_006090 | EEG Toolbox | 2026-09-05 06:30:41 | 1 | |||||||
|
GeneVenn Resource Report Resource Website 100+ mentions |
GeneVenn (RRID:SCR_012117) | analysis service resource, data analysis service, production service resource, service resource | A web application creating Venn diagrams from two or three gene lists. | web app |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:17597932 | OMICS_05568 | SCR_012117 | 2026-09-05 06:32:02 | 107 | |||||||||
|
OBO Tracker: Plant Ontology (PO) TERM requests Resource Report Resource Website 1+ mentions |
OBO Tracker: Plant Ontology (PO) TERM requests (RRID:SCR_006497) | OBO SF PO | data or information resource, database | Open Biomedical Ontologies Tracker that allows users to browse the Plant Ontology (PO) term requests and view their status. Details include a summary, ID, status, Date opened, assignee, submitter, resolution and assigned priority. New requests are accepted from logged in users. | plant, ontology, term |
is related to: OBO has parent organization: SourceForge |
The community can contribute to this resource, Account required | nlx_99576 | SCR_006497 | Tracker: PO TERM requests, Tracker: Plant Ontology TERM requests, SourceForge.net: Open Biomedical Ontologies: Plant Ontology (PO) TERM requests, Source Forge OBO Plant Ontology (PO) term request tracker, Tracker: Plant Ontology (PO) TERM requests | 2026-09-05 06:31:35 | 2 | |||||||
|
Hanalyzer Resource Report Resource Website |
Hanalyzer (RRID:SCR_000923) | software application, software resource, source code | An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download. | genomic, visualization, reading, reasoning, reporting, throughput analyzer, data network |
has parent organization: University of Colorado Denver; Colorado; USA has parent organization: SourceForge |
NIDCR R01DE15191; NLM R01LM008111; NLM R01LM009254; NIGMS R01GM083649; NLM T15LM009451; NHGRI 5R01HG004483-09 |
PMID:19325874 | nlx_48287 | SCR_000923 | Hanalyzer: A 3R System | 2026-09-05 06:31:12 | 0 | |||||||
|
CHEBI Resource Report Resource Website 100+ mentions |
CHEBI (RRID:SCR_002088) | ChEBI | data or information resource, database | Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. | complex, conformer, ion, ion pair, isotope, molecular entity, molecule, radical, radical ion, small molecule, obo, gold standard, biochemistry, metabolomics, bio.tools |
uses: IUPAC uses: Nomenclature Committee of IUBMB is used by: Open PHACTS is used by: Ultimate Rough Aggregation of Metabolic Map is used by: RHEA is used by: GEROprotectors is used by: SwissLipids is listed by: OBO is listed by: BioPortal is listed by: NIF Data Federation is listed by: SourceForge is listed by: bio.tools is listed by: Debian is related to: Pathway Commons is related to: Integrated Manually Extracted Annotation has parent organization: European Bioinformatics Institute is parent organization of: Physico-Chemical Process is parent organization of: Physico-Chemical Methods and Properties works with: MiMeDB |
BBSRC BB/G022747/1 | PMID:19854951 PMID:19496059 PMID:17932057 |
Freely available | nif-0000-02655, biotools:chebi, r3d100012626 | http://bioportal.bioontology.org/ontologies/1007, http://www.obofoundry.org/cgi-bin/detail.cgi?id=chebi, ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo, http://chebi.wiki.sourceforge.net/, https://bio.tools/chebi | http://www.ebi.ac.uk/chebi/ | SCR_002088 | CHEBI, Chemical Entities of Biological Interest | 2026-09-05 06:31:16 | 129 | |||
|
MarsBaR region of interest toolbox for SPM Resource Report Resource Website 1000+ mentions |
MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) | MarsBaR | data processing software, software application, software resource, software toolkit | A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery. | analyze, linear, matlab, magnetic resonance, nifti, os independent, regression, statistical operation, region of interest, spm, analysis |
is used by: BetA-Series COrrelation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: SourceForge |
GNU General Public License | nlx_155806 | http://www.nitrc.org/projects/marsbar | SCR_009605 | MARSeille Boite A Region dInteret, MARSeille Boite a Region dInteret | 2026-09-05 06:30:46 | 1320 | ||||||
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PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software application, software resource | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-09-05 06:32:22 | 0 | ||||||
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Magnolya Resource Report Resource Website 1+ mentions |
Magnolya (RRID:SCR_000164) | data analytics software, software application, software resource | A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets. | algorithm, copy number, next-generation, reference genome, dataset comparison |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23047563 | Free, Available for download, Freely available | OMICS_00347 | SCR_000164 | 2026-09-05 06:32:20 | 2 | ||||||||
|
UTR Resource Report Resource Website |
UTR (RRID:SCR_000045) | software application, software resource, standalone software | Software application that uses change point model for detecting 3-prime UTR changes by RNA-Seq. | java, 3 prime utr, rna sequence, change point model, detecting 3-prime UTR changes, RNA-Seq |
uses: R Project for Statistical Computing has parent organization: SourceForge |
PMID:24728858 | Free, Available for download, Freely available | OMICS_04052 | SCR_000045 | 2026-09-05 06:32:20 | 0 | ||||||||
|
mzMatch Resource Report Resource Website 1+ mentions |
mzMatch (RRID:SCR_000543) | software resource, software toolkit | A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java. | metabolomics, analysis, java, tool, peak extraction, filtering, normalization, derivative detection, identification, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23162054 | Free, Available for download, Freely available, | biotools:mzmatch, OMICS_02642 | https://bio.tools/mzmatch | SCR_000543 | 2026-09-05 06:32:21 | 5 | |||||||
|
metabnorm Resource Report Resource Website |
metabnorm (RRID:SCR_001266) | software application, software resource, standalone software | Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix. | Metabolomics datasets, corelation, normalization, identifying metabolites, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
Cancer Research UK Cambridge Institute ; Cancer Research UK ; Erik and Edith Fernström foundation |
PMID:24711654 | Free, Available for download, Freely available | OMICS_03548, biotools:metabnorm | https://bio.tools/metabnorm | SCR_001266 | 2026-09-05 06:32:24 | 0 |
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