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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | https://bio.tools/gprege | SCR_001324 | Gaussian Process Ranking and Estimation of Gene Expression time-series | 2025-04-09 11:47:03 | 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 | biotools:kanalyze, OMICS_03565 | https://bio.tools/kanalyze | SCR_001323 | 2025-04-09 11:47:03 | 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 | 2025-04-09 11:47:02 | 116 | |||||
|
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 | Artistic License, v2 | OMICS_01989, biotools:macat | https://bio.tools/macat | SCR_001350 | MicroArray Chromosome Analysis Tool | 2025-04-09 11:47:05 | 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 |
GNU General Public License, v2 or newer | biotools:lapmix, OMICS_01992 | https://bio.tools/lapmix | SCR_001347 | Laplace Mixture Model in Microarray Experiments | 2025-04-09 11:47:05 | 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 | Acknowledgement requested | OMICS_01995, biotools:farms | https://bio.tools/farms | SCR_001344 | Factor Analysis for Robust Microarray Summarization | 2025-04-09 11:47:04 | 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 | GNU General Public License, v2 or newer | OMICS_01996, biotools:bridge | https://bio.tools/bridge | SCR_001343 | Bayesian Robust Inference for Differential Gene Expression | 2025-04-09 11:47:04 | 136 | |||||
|
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 | 2025-04-09 11:47:02 | 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 | GNU General Public License, v2 | biotools:beaddatapackr, OMICS_02023 | https://bio.tools/beaddatapackr | SCR_001310 | BeadDataPackR - Compression of Illumina BeadArray data | 2025-04-09 11:47:02 | 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 | GNU General Public License, v2 | biotools:olin, OMICS_02029 | https://bio.tools/olin | SCR_001304 | Optimised Local Intensity-dependent Normalisation | 2025-04-09 11:47:01 | 17 | |||||
|
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 |
GNU General Public License, v2 | 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 | 2025-04-09 11:47:01 | 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 | GNU Lesser General Public License, v2 or newer | biotools:dexus, OMICS_02024 | https://bio.tools/dexus | SCR_001309 | DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates | 2025-04-09 11:47:02 | 1 | |||||
|
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, Non-commercial use | OMICS_00423, biotools:cisgenome | https://bio.tools/cisgenome | http://biogibbs.stanford.edu/~jihk/CisGenome/index.htm | SCR_001558 | CisGenome v2.0 | 2025-04-09 11:47:23 | 80 | |||||
|
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 |
Artistic License, v2 | OMICS_01977, biotools:vsn | https://bio.tools/vsn | SCR_001459 | vsn - Variance stabilization and calibration for microarray data | 2025-04-09 11:47:14 | 3 | ||||||
|
InterMine Resource Report Resource Website 10+ mentions |
InterMine (RRID:SCR_001772) | software resource | An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data. | 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: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust | PMID:24753429 | GNU Lesser General Public License, v2 | OMICS_03840, biotools:intermine | https://github.com/intermine/intermine https://bio.tools/intermine |
SCR_001772 | 2025-04-09 11:47:44 | 20 | ||||||
|
unifiedWMWqPCR Resource Report Resource Website |
unifiedWMWqPCR (RRID:SCR_001706) | software resource | Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data. | standalone software, mac os x, unix/linux, windows, r, gene expression, microtitre plate assay, qpcr, differential expression, multiple comparison, quality control, visualization, qpcr, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24794933 | GNU General Public License, v2 or greater | OMICS_03937, biotools:unifiedwmwqpcr | https://bio.tools/unifiedwmwqpcr | SCR_001706 | unifiedWMWqPCR - Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data | 2025-04-09 11:47:37 | 0 | ||||||
|
CCAT Resource Report Resource Website 50+ mentions |
CCAT (RRID:SCR_001843) | CCAT | software resource | THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Genome Institute of Singapore; Singapore; Singapore |
PMID:20371496 | OMICS_00428, biotools:ccat | https://bio.tools/ccat | SCR_001843 | Control based ChIP-Seq Analysis Tools | 2025-04-09 11:47:52 | 66 | ||||||
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S-MART Resource Report Resource Website 10+ mentions |
S-MART (RRID:SCR_001908) | S-MART | software resource | Software toolbox that manages your RNA-Seq and ChIP-Seq data and also produces many different plots to visualize your data. It performs several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization. It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis. It also provides many ways to visualize data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots). A computer science background is not required to run it through a graphical interface and it can be run on any personal computer, yielding results within an hour for most queries. | high throughput sequencing, rna-seq, chip-seq, python, linux, ms windows, mac, short-read, selection, visualization, bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21998740 | OMICS_01937, biotools:mapperanalyzer, biotools:s-mart | https://bio.tools/s-mart https://bio.tools/mapperanalyzer |
SCR_001908 | 2025-04-09 11:47:59 | 23 | |||||||
|
SamSPECTRAL Resource Report Resource Website 1+ mentions |
SamSPECTRAL (RRID:SCR_001858) | software resource | Software that identifies cell population in flow cytometry data. It demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. It samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample. | software package, mac os x, unix/linux, windows, r, cell biology, clustering, flow cytometry, stem cell, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Cancer, HIV | PMID:20667133 | GNU General Public License, v2 or greater | OMICS_05638, biotools:samspectral | https://bio.tools/samspectral | SCR_001858 | SamSPECTRAL - Identifies cell population in flow cytometry data | 2025-04-09 11:47:53 | 4 | |||||
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CQN Resource Report Resource Website 1+ mentions |
CQN (RRID:SCR_001786) | CQN | software resource | A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. | rna-seq, differential expression, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
PMID:22285995 | Artistic License, v3 | OMICS_01949, biotools:cqn | https://bio.tools/cqn | SCR_001786 | Conditional Quantile Normalization | 2025-04-09 11:47:46 | 6 |
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