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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
QuickGO Resource Report Resource Website 500+ mentions |
QuickGO (RRID:SCR_004608) | QuickGO | controlled vocabulary, data access protocol, data or information resource, database, ontology, software resource, web service | A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services. | gene, ontology, annotation, browser, visualization, search engine, slimmer-type tool, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, windows, mac os x, linux, unix, gold standard, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: STRAP has parent organization: European Bioinformatics Institute |
BBSRC BB/E023541/1 | PMID:19744993 PMID:20157483 |
Apache License, v2, Free for academic use | biotools:quickgo, nlx_60318, OMICS_02276 | https://bio.tools/quickgo | SCR_004608 | Quick GO | 2026-09-12 12:56:14 | 556 | ||||
|
ShoRAH Resource Report Resource Website 10+ mentions |
ShoRAH (RRID:SCR_005211) | ShoRAH | software resource | A software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. | linux, mac os x, windows, next-generation sequencing, c++, python, perl, structure, population, short sequence read, haplotype, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:21521499 | GNU General Public License, v3 | biotools:shorah, OMICS_00231 | https://bio.tools/shorah | SCR_005211 | Short Reads Assembly into Haplotypes, ShoRAH - Short Reads Assembly into Haplotypes | 2026-09-12 12:56:22 | 36 | |||||
|
DMRforPairs Resource Report Resource Website 1+ mentions |
DMRforPairs (RRID:SCR_005702) | software resource | Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance. | standalone software, mac os x, unix/linux, windows, r, annotation, dna methylation, differential methylation, microarray, report writing, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24884391 | GNU General Public License, v2 or greater | biotools:dmrforpairs, OMICS_04059 | https://bio.tools/dmrforpairs | SCR_005702 | DMR2+, DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles | 2026-09-12 12:56:30 | 4 | ||||||
|
GoFish Resource Report Resource Website 1+ mentions |
GoFish (RRID:SCR_005682) | GoFish | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, ontology or annotation browser, java, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA |
Aventis Pharmaceuticals ; Howard Hughes Medical Institute ; NHGRI |
PMID:12691998 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gofish, nlx_149126, OMICS_02272 | http://llama.mshri.on.ca/Software.html, https://bio.tools/gofish | SCR_005682 | 2026-09-12 12:56:29 | 1 | |||||
|
MIMOSA Resource Report Resource Website |
MIMOSA (RRID:SCR_000184) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23887981 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mimosa, OMICS_05642 | https://bio.tools/mimosa | SCR_000184 | MIMOSA - Mixture Models for Single-Cell Assays, MIMOSA: Mixture Models For Single Cell Assays | 2026-09-12 12:55:04 | 0 | ||||||
|
iASeq Resource Report Resource Website |
iASeq (RRID:SCR_000420) | software resource | Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins. | software package, unix/linux, mac os x, windows, r, chip-seq, rna-seq, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23194258 | Free, Available for download, Freely available | OMICS_05505 | SCR_000420 | iASeq: integrating multiple sequencing datasets for detecting allele-specific events | 2026-09-12 12:55:09 | 0 | |||||||
|
rTANDEM Resource Report Resource Website |
rTANDEM (RRID:SCR_000409) | software resource | An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, proteomics |
is used by: shinyTANDEM is listed by: OMICtools has parent organization: Bioconductor |
PMID:24700319 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03516 | SCR_000409 | rTANDEM - Interfaces the tandem protein identification algorithm in R | 2026-09-12 12:55:08 | 0 | |||||||
|
flowPeaks Resource Report Resource Website |
flowPeaks (RRID:SCR_000407) | software resource | Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, gating, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:22595209 | Free, Available for download, Freely available | biotools:flowpeaks, OMICS_05604 | http://www.bioconductor.org/packages/devel/bioc/html/flowPeaks.html, https://bio.tools/flowpeaks | SCR_000407 | 2026-09-12 12:55:08 | 0 | |||||||
|
QUALIFIER Resource Report Resource Website |
QUALIFIER (RRID:SCR_000389) | software resource | Software that provides quality control and quality assessment tools for gated 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 |
PMID:23020243 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05618 | SCR_000389 | QUALIFIER - Quality Control of Gated Flow Cytometry Experiments | 2026-09-12 12:55:08 | 0 | |||||||
|
Rdisop Resource Report Resource Website |
Rdisop (RRID:SCR_000453) | software resource | Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02416, biotools:rdisop | https://github.com/sneumann/Rdisop, https://bio.tools/rdisop | SCR_000453 | Rdisop - Decomposition of Isotopic Patterns, Rdisop: Decomposition of Isotopic Patterns, Decomposition of Isotopic Patterns | 2026-09-12 12:55:09 | 0 | |||||||
|
FlipFlop Resource Report Resource Website |
FlipFlop (RRID:SCR_000625) | software resource | Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. | standalone software, unix/linux, mac os x, windows, r, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24813214 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04028, biotools:flipflop | https://bio.tools/flipflop | SCR_000625 | flipflop - Fast lasso-based isoform prediction as a flow problem | 2026-09-12 12:55:12 | 0 | ||||||
|
PiNGO Resource Report Resource Website |
PiNGO (RRID:SCR_000692) | PiNGO | software resource | A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, annotation, network, candidate gene, biological network, ontology or annotation search engine, statistical analysis, term enrichment, functional similarity, functional prediction, search engine, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Cytoscape has parent organization: Ghent University; Ghent; Belgium |
PMID:21278188 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149330, OMICS_02281 | SCR_000692 | 2026-09-12 12:55:13 | 0 | |||||||
|
jmzML Resource Report Resource Website 1+ mentions |
jmzML (RRID:SCR_001119) | software resource | A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard. | standalone software, 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: Google Code |
PMID:20127693 | Free, Available for download, Freely available | biotools:jmzml, OMICS_03340 | https://bio.tools/jmzml | SCR_001119 | 2026-09-12 12:55:19 | 1 | |||||||
|
massiR Resource Report Resource Website |
massiR (RRID:SCR_001157) | software resource | Software that predicts the sex of samples in gene expression microarray datasets. | standalone software, mac os x, unix/linux, windows, r, classification, clustering, gene expression, microarray, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24659105 | Free, Available for download, Freely available | biotools:massir, OMICS_03638 | https://bio.tools/massir | SCR_001157 | massiR: MicroArray Sample Sex Identifier, MicroArray Sample Sex Identifier | 2026-09-12 12:55:20 | 0 | ||||||
|
DSS Resource Report Resource Website 1+ mentions |
DSS (RRID:SCR_002754) | software library, software resource, software toolkit | Software R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions. | standalone software, unix/linux, mac os x, windows, r, differential expression, rna-seq, chip-seq, dna methylation, differential expression, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24561809 | Free, Freely available, Available for download | OMICS_03273 | SCR_002754 | Dispersion Shrinakge for Sequencing data, DSS - Dispersion shrinakge for sequencing data | 2026-09-12 12:55:46 | 9 | |||||||
|
rBiopaxParser Resource Report Resource Website 1+ mentions |
rBiopaxParser (RRID:SCR_002744) | software resource | A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported. | software package, mac os x, unix/linux, windows, data representation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23274212 | Free, Freely available, Available for download | biotools:rbiopaxparser, OMICS_05211 | https://github.com/frankkramer/rBiopaxParser, https://bio.tools/rbiopaxparser | SCR_002744 | rBiopaxParser - Parses BioPax files and represents them in R | 2026-09-12 12:55:45 | 4 | ||||||
|
aCGH.Spline Resource Report Resource Website |
aCGH.Spline (RRID:SCR_002927) | software resource | An R package for array comparative genomic hybridization (aCGH) dye bias normalization. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21357574 | Free, Available for download, Freely available | OMICS_02607 | http://cran.r-project.org/web/packages/aCGH.Spline/ | SCR_002927 | 2026-09-12 12:55:48 | 0 | |||||||
|
Basic4Cseq Resource Report Resource Website 1+ mentions |
Basic4Cseq (RRID:SCR_002836) | software resource | An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile. | software package, unix/linux, mac os x, windows, r, quality control, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25078398 | Free, Freely available, Available for download | OMICS_05202 | SCR_002836 | Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data | 2026-09-12 12:55:47 | 6 | |||||||
|
mzR Resource Report Resource Website 1+ mentions |
mzR (RRID:SCR_002856) | software resource | Software that provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. | standalone software, mac os x, unix/linux, windows, r, data import, infrastructure, mass spectrometry, metabolomics, proteomics |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available, Available for download | OMICS_02654 | SCR_002856 | mzR - parser for netCDF mzXML mzData and mzML and mzIdentML files | 2026-09-12 12:55:47 | 1 | ||||||||
|
BiGGR Resource Report Resource Website |
BiGGR (RRID:SCR_002854) | software resource | Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs. | standalone software, mac os x, unix/linux, windows, r, metabolomics, network, visualization, metabolic reconstruction, model |
uses: BiGG Database is listed by: OMICtools has parent organization: Bioconductor |
PMID:25806817 | Free, Freely available, Available for download | OMICS_02655 | SCR_002854 | BiGGR - Constraint based modeling in R using metabolic reconstruction databases | 2026-09-12 12:55:47 | 0 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
