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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SEER Resource Report Resource Website 500+ mentions |
SEER (RRID:SCR_015499) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Sequence element enrichment analysis tool to perform pan-genome-wide association studies in bacteria. | bacterial genome association, sequence element enrichment analysis, kmer enrichment analysis |
is listed by: Debian is listed by: OMICtools is hosted by: GitHub |
DOI:10.1038/ncomms12797 DOI:10.1101/038463 |
Available for download | OMICS_21699 | https://sources.debian.org/src/seer/ | SCR_015499 | 2026-09-05 06:27:56 | 547 | |||||||
|
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 | 2026-09-05 06:24:33 | 1 | |||||
|
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 | 2026-09-05 06:24:33 | 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 | 2026-09-05 06:24:32 | 123 | |||||
|
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 | 2026-09-05 06:24:33 | 0 | |||||
|
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 | 2026-09-05 06:24:33 | 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 | 2026-09-05 06:24:33 | 28 | |||||
|
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 | 2026-09-05 06:24:33 | 157 | |||||
|
vsn Resource Report Resource Website 1+ mentions |
vsn (RRID:SCR_001459) | vsn | software resource | Software package that implements a method for normalizing microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (a.k.a. normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to normalized log-ratios. However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription. | microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
Free, Available for download, Freely available | OMICS_01977, biotools:vsn | https://bio.tools/vsn | SCR_001459 | vsn - Variance stabilization and calibration for microarray data | 2026-09-05 06:24:34 | 6 | ||||||
|
UNAFold Resource Report Resource Website 100+ mentions |
UNAFold (RRID:SCR_001360) | data analysis software, data processing software, software application, software resource | Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows. | software, nucleic acid, folding, hybridization, prediction, rna, dna, stochastic sampling, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University at Albany; New York; USA |
Free, Available for download, Freely available | biotools:unafold, nif-0000-07753 | http://mfold.rna.albany.edu/ | SCR_001360 | The UNAFold Web Server, UNAFold Web Server | 2026-09-05 06:24:33 | 373 | |||||||
|
Happy Resource Report Resource Website 10+ mentions |
Happy (RRID:SCR_001395) | HAPPY | data analysis software, data processing software, software application, software resource, source code | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download). | qtl, quantitative trait locus, r, c, gene, genetic, genomic, ansi c, unix, irix, sunos, linux, animal model, trait, map, genotype, phenotype, haplotype, linear regression, data set, qtl mapping |
is listed by: Genetic Analysis Software is listed by: Debian has parent organization: Wellcome Trust Centre for Human Genetics |
Wellcome Trust | PMID:11050180 DOI:10.1073/pnas.230304397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152594 | http://www.well.ox.ac.uk/~rmott/happy.html | https://sources.debian.org/src/r-other-mott-happy.hbrem/ | SCR_001395 | reconstructing HAPlotYpes | 2026-09-05 06:24:34 | 46 | |||
|
aroma.light Resource Report Resource Website 1+ mentions |
aroma.light (RRID:SCR_001312) | aroma.light | software resource | Light-weight software package for normalization and visualization of microarray data using only basic R data types. Software can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. | infrastructure, microarray, preprocessing, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
DOI:10.1186/1471-2105-11-245 | Free, Available for download, Freely available | OMICS_01998, biotools:aroma.light | https://bio.tools/aroma.light, https://sources.debian.org/src/r-bioc-aroma.light/ | SCR_001312 | 2026-09-05 06:24:32 | 1 | ||||||
|
BeadDataPackR Resource Report Resource Website |
BeadDataPackR (RRID:SCR_001310) | BeadDataPackR | software resource | Software that provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform. | microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:20981138 | Free, Available for download, Freely available | biotools:beaddatapackr, OMICS_02023 | https://bio.tools/beaddatapackr | SCR_001310 | BeadDataPackR - Compression of Illumina BeadArray data | 2026-09-05 06:24:32 | 0 | |||||
|
OLIN Resource Report Resource Website 10+ mentions |
OLIN (RRID:SCR_001304) | OLIN | software resource | Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data. | r, normalization, visualization, quality control, two-channel, microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:15585527 | Free, Available for download, Freely available | biotools:olin, OMICS_02029 | http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html | SCR_001304 | Optimised Local Intensity-dependent Normalisation | 2026-09-05 06:24:32 | 18 | |||||
|
qcmetrics Resource Report Resource Website 1+ mentions |
qcmetrics (RRID:SCR_001303) | qcmetrics | software resource | Software package that provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats. | mass spectrometry, microarray, proteomics, quality control, visualization, 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 | OMICS_02032, biotools:qcmetrics, BioTools:qcmetrics | https://bio.tools/qcmetrics, https://bio.tools/qcmetrics, https://bio.tools/qcmetrics | SCR_001303 | qcmetrics - A Framework for Quality Control | 2026-09-05 06:24:32 | 1 | ||||||
|
DEXUS Resource Report Resource Website 1+ mentions |
DEXUS (RRID:SCR_001309) | DEXUS | software resource | Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power. | classification, differential expression, gene expression, hapmap, quality control, rna-seq, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24049071 | Free, Available for download, Freely available | biotools:dexus, OMICS_02024 | http://www.bioconductor.org/packages/release/bioc/html/dexus.html | SCR_001309 | DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates | 2026-09-05 06:24:32 | 1 | |||||
|
Mugsy Resource Report Resource Website 50+ mentions |
Mugsy (RRID:SCR_001414) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy. | software, genome, genome alignment, segmentation, pairwise alignment, sequence analysis software |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:21148543 DOI:10.1093/bioinformatics/btq665 |
Free, Available for download, Freely available | OMICS_03606 | https://sources.debian.org/src/mugsy/ | SCR_001414 | 2026-09-05 06:24:34 | 75 | |||||||
|
Enrichr Resource Report Resource Website 5000+ mentions |
Enrichr (RRID:SCR_001575) | Enrichr | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | A web-based gene list enrichment analysis tool that provides various types of visualization summaries of collective functions of gene lists. It includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes / proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. | bed, gene, software as a service, rna-seq, analyze, protein, function, gene list, visualization, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:23586463 | Free, Freely available | biotools:enrichr, SciRes_000171 | https://bio.tools/enrichr | SCR_001575 | 2026-09-05 06:24:36 | 5047 | ||||||
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CisGenome Resource Report Resource Website 50+ mentions |
CisGenome (RRID:SCR_001558) | data analysis tool | Integrated software tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis. | sequencing software, chip seq, downstream analysis, chip analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian works with: TileMap |
PMID:18978777 | Free, Available for download, Freely available | OMICS_00423, biotools:cisgenome | https://bio.tools/cisgenome | http://biogibbs.stanford.edu/~jihk/CisGenome/index.htm | SCR_001558 | CisGenome v2.0 | 2026-09-05 06:24:36 | 83 | |||||
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DNACLUST Resource Report Resource Website 1+ mentions |
DNACLUST (RRID:SCR_001771) | software resource | Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads. | cluster, dna sequence, gene, 16s rrna pyrosequencing read, microbiome |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian has parent organization: SourceForge |
PMID:21718538 DOI:10.1186/1471-2105-12-271 |
Free, Available for download, Freely available | OMICS_01955 | https://sources.debian.org/src/dnaclust/ | SCR_001771 | DNAClust | 2026-09-05 06:24:39 | 9 |
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