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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Roche Resource Report Resource Website 500+ mentions |
Roche (RRID:SCR_001326) | commercial organization | A Swiss global health-care company that operates under two divisions: Pharmaceuticals and Diagnostics. | pharmaceutical, diagnostic, drug, medicine, commercial |
is affiliated with: European Federation of Pharmaceutical Industries and Associations is related to: EU-AIMS is related to: eTRIKS is related to: OncoTrack is related to: GetReal is related to: IMIDIA is related to: Kinetics for Drug Discovery is related to: NEWMEDS is related to: PharmaCog is related to: PREDECT is related to: EMIF is parent organization of: EU-AIMS is parent organization of: Genentech is parent organization of: Roche Diagnostics is parent organization of: Roche: cobas�� e 601 |
ISNI: 0000 0004 1759 0967, grid.486917.5, nlx_152451, Wikidata: Q41568432 | https://ror.org/02hv5e369 | SCR_001326 | Hoffmann-La Roche AG, Hoffmann-La Roche, Roche Holding AG, F. Hoffmann-La Roche, F. Hoffmann-La Roche Ltd | 2026-08-01 12:01:48 | 502 | ||||||||
|
gprege Resource Report Resource Website 1+ mentions |
gprege (RRID:SCR_001324) | gprege | software resource | Software R package for Gaussian Process Ranking and Estimation of Gene Expression time-series. The software fits two Gaussian processes (GPs) with an radial basis function (RBF) (+ noise diagonal) kernel on each profile. One GP kernel is initialized wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimized via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via receiver operating characteristic curves (ROC curves) is performed against Bayesian hierarchical model for the analysis of time-series (BATS) (Angelini et.al, 2007). | differential expression, microarray, preprocessing, time course, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:21599902 | Free, Available for download, Freely available | OMICS_02011, biotools:gprege | http://www.bioconductor.org/packages/release/bioc/html/gprege.html | SCR_001324 | Gaussian Process Ranking and Estimation of Gene Expression time-series | 2026-08-01 12:01:38 | 1 | |||||
|
waveTiling Resource Report Resource Website |
waveTiling (RRID:SCR_001322) | waveTiling | software resource | Software package to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models. | differential expression, microarray, gene expression, time course |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22974078 | Free, Available for download, Freely available | OMICS_02014 | http://www.bioconductor.org/packages/release/bioc/html/waveTiling.html | SCR_001322 | waveTiling - Wavelet-Based Models for Tiling Array Transcriptome Analysis | 2026-08-01 12:01:27 | 0 | |||||
|
KAnalyze Resource Report Resource Website 1+ mentions |
KAnalyze (RRID:SCR_001323) | software resource | A Java toolkit designed to convert DNA and RNA sequences into k-mers. | standalone software, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24642064 | Free, Available for download, Freely available | biotools:kanalyze, OMICS_03565 | https://bio.tools/kanalyze | SCR_001323 | 2026-08-01 12:01:47 | 2 | |||||||
|
AffyExpress Resource Report Resource Website 1+ mentions |
AffyExpress (RRID:SCR_001321) | AffyExpress | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data. | differential expression, microarray, annotation, one channel, preprocessing, quality control, report writing, visualization, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02015 | SCR_001321 | AffyExpress - Affymetrix Quality Assessment and Analysis Tool | 2026-08-01 12:01:38 | 2 | |||||||
|
beadarray Resource Report Resource Website 100+ mentions |
beadarray (RRID:SCR_001314) | beadarray | software resource | Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. | microarray, quality control, one channel, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
PMID:17586828 | GNU General Public License, v2 | OMICS_02021, biotools:beadarray | https://bio.tools/beadarray | SCR_001314 | beadarray - Quality assessment and low-level analysis for Illumina BeadArray data | 2026-08-01 12:01:38 | 119 | |||||
|
arrayMvout Resource Report Resource Website 1+ mentions |
arrayMvout (RRID:SCR_001317) | arrayMvout | software resource | Software package that supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate. | infrastructure, microarray, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02019 | SCR_001317 | arrayMvout - Multivariate outlier detection for expression array QA | 2026-08-01 12:01:47 | 1 | |||||||
|
affyQCReport Resource Report Resource Website 10+ mentions |
affyQCReport (RRID:SCR_001318) | affyQCReport | software resource | Software package to create a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object. | microarray, one channel, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02018 | http://www.bioconductor.org/packages/release/bioc/html/affyQCReport.html | SCR_001318 | affyQCReport - QC Report Generation for affyBatch objects | 2026-08-01 12:01:38 | 44 | ||||||
|
maigesPack Resource Report Resource Website |
maigesPack (RRID:SCR_001351) | maigesPack | software resource | Software package that uses functions to handle and analyze cDNA microarray data. | classification, clustering, differential expression, graph, network, microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01988 | http://www.bioconductor.org/packages/release/bioc/html/maigesPack.html | SCR_001351 | 2026-08-01 12:01:28 | 0 | |||||||
|
MDQC Resource Report Resource Website |
MDQC (RRID:SCR_001352) | MDQC | software resource | A multivariate quality assessment software for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality. | microarray, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:17933854 | Free, Available for download, Freely available | OMICS_01987 | SCR_001352 | Mahalanobis Distance Quality Control for microarrays | 2026-08-01 12:01:49 | 0 | ||||||
|
MACAT Resource Report Resource Website |
MACAT (RRID:SCR_001350) | MACAT | software resource | Software library that contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. It is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. | differential expression, microarray, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:15572464 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01989, biotools:macat | https://bio.tools/macat | SCR_001350 | MicroArray Chromosome Analysis Tool | 2026-08-01 12:01:39 | 0 | |||||
|
nnNorm Resource Report Resource Website |
nnNorm (RRID:SCR_001354) | nnNorm | software resource | Software package that allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01985 | SCR_001354 | nnNorm - Spatial and intensity based normalization of cDNA microarray data based on robust neural nets | 2026-08-01 12:01:28 | 0 | |||||||
|
maCorrPlot Resource Report Resource Website 1+ mentions |
maCorrPlot (RRID:SCR_001348) | maCorrPlot | software resource | Software that graphically displays correlation in microarray data that is due to insufficient normalization. | microarray, preprocessing, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:15799785 | Free, Available for download, Freely available | OMICS_01991 | SCR_001348 | maCorrPlot - Visualize artificial correlation in microarray data | 2026-08-01 12:01:28 | 2 | ||||||
|
lapmix Resource Report Resource Website |
lapmix (RRID:SCR_001347) | lapmix | software resource | Software to identify differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. | differential expression, microarray, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:lapmix, OMICS_01992 | https://bio.tools/lapmix | SCR_001347 | Laplace Mixture Model in Microarray Experiments | 2026-08-01 12:01:39 | 0 | ||||||
|
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 | 2026-08-01 12:01:39 | 28 | |||||
|
OCplus Resource Report Resource Website 1+ mentions |
OCplus (RRID:SCR_001342) | OCplus | software resource | Software package that allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). | differential expression, microarray, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16368770 | Free, Available for download, Freely available | OMICS_01999 | SCR_001342 | Ocplus - Operating characteristics plus sample size and local fdr for microarray experiments | 2026-08-01 12:01:28 | 1 | ||||||
|
bridge Resource Report Resource Website 100+ mentions |
bridge (RRID:SCR_001343) | bridge | software resource | Software package to test for differentially expressed genes with microarray data. It can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. The model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space. | cdna microarray, affymetrix chip, differential expression, microarray, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:16542223 | Free, Available for download, Freely available | OMICS_01996, biotools:bridge | http://www.bioconductor.org/packages/release/bioc/html/bridge.html | SCR_001343 | Bayesian Robust Inference for Differential Gene Expression | 2026-08-01 12:01:48 | 156 | |||||
|
CALIB Resource Report Resource Website 100+ mentions |
CALIB (RRID:SCR_001338) | CALIB | software resource | Software package that contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:17485432 | Free, Available for download, Freely available | OMICS_02003 | http://www.bioconductor.org/packages/release/bioc/html/CALIB.html | SCR_001338 | 2026-08-01 12:01:39 | 136 | ||||||
|
Brede Wiki Resource Report Resource Website |
Brede Wiki (RRID:SCR_001411) | narrative resource, data or information resource, wiki | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 10, 2025. Semantic wiki with structured information, primarily from functional and molecular neuroimaging papers, but there are also other types of papers, e.g., from personality genetics. It lists results from neuroimaging studies, such as Talairach coordinates and brain volume measurements, as well as software packages and brain regions. SQL dumps of the structured information in the wiki is available so complex queries can be formed. The Brede Wiki templates store the structured information from neuroscience papers and editors may add free format text. Template definitions format the data so it is presented as tables on the formatted wiki-page. From a given PMID a web-service can format information from PubMed for inclusion in the Brede Wiki. A Matlab script can extract coordinates from SPM5 and format them in the Talairach coordinate template format. | neuroinformatics, neuroscience, functional neuroimaging, molecular neuroimaging, fmri, mri, talairach, brain region, data sharing, mediawiki, sql |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Brede Database is related to: Brede Toolbox is related to: Brede Database has parent organization: Technical University of Denmark; Lyngby; Denmark |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-08130 | http://www.nitrc.org/projects/bredewiki | SCR_001411 | Brede Wiki - a neuroinformatics wiki | 2026-08-01 12:01:29 | 0 | |||||||
|
Integrated Content Environment Resource Report Resource Website |
Integrated Content Environment (RRID:SCR_001369) | ICE | collaboration tool, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The Integrated Content Environment (ICE) is a free Word-processor based system that allows authors to work individually or collaboratively on material for the Web, CD and print. This free web content management system, produced by the University of Southern Queensland, was initially developed by staff at the university to produce course content for online and print delivery. It has also been used for general web site development, and to manage documents in project intranets. | integrated content, word processor, collaboration, content management | has parent organization: University of Southern Queensland; Queensland; Australia | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-07757 | http://ice.usq.edu.au/default.htm https://eprints.usq.edu.au/697/ | http://www.usq.edu.au/lrds/tech/ice | SCR_001369 | Integrated Content Environment (ICE) | 2026-08-01 12:01:50 | 0 |
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