Allows the user to select genes that represent given functional categories.…
Allows the user to select genes that represent given functional categories. Onto-Design permits to create customized array representing some chosen biological processes. It provides the means to…
Provides lists of differentially expressed genes. L2L was constructed by…
Provides lists of differentially expressed genes. L2L was constructed by compiling data from published mammalian microarray studies. It contains a set of lists for each of the three organizing…
Enables biology researchers to explore the entirety of very large microarray…
Enables biology researchers to explore the entirety of very large microarray compendia in a biologically meaningful manner. SPELL is a scalable, context-specific search methodology implemented in an…
Integrates different multiscale algorithms for binarization and for…
Integrates different multiscale algorithms for binarization and for trinarization of one-dimensional data with methods for quality assessment and visualization of the results. By identifying…
Provides a method for researchers to predict the sex of samples in microarray…
Provides a method for researchers to predict the sex of samples in microarray datasets.
Implements a method for characterizing cell composition of complex tissues from…
Implements a method for characterizing cell composition of complex tissues from their gene expression profiles. CIBERSORT requires an input matrix of reference gene expression signatures,…
An R-package to simulate gene expression and DNA methylation data. The…
An R-package to simulate gene expression and DNA methylation data. The R-package quantroSim is the supporting data simulation package for the quantro R/Bioconductor package which can be used to…
Predicts tissue/cell type marker genes using microarray gene expression data.…
Predicts tissue/cell type marker genes using microarray gene expression data. The main advantages of MGFM are i) a short running time of some seconds per analysis. This is achieved by sorting the…
Combines connectivity and expression data to produce a robust summary of an…
Combines connectivity and expression data to produce a robust summary of an experiment. GeneRank is based on the PageRank algorithm and increase its capabilities to rank genes in microarray…
Enables cross-platform comparisons, and proposes a comprehensive procedure for…
Enables cross-platform comparisons, and proposes a comprehensive procedure for assessments based on spike-in experiments. spkTools is implemented as a user friendly Bioconductor package. It contains…
Estimates gene and eQTL networks from high-throughput expression and genotyping…
Estimates gene and eQTL networks from high-throughput expression and genotyping assays. qpgraph is based in the so-called q-order limited partial correlation graphs, qp-graphs, which is specifically…
Follows the expression based karyotyping workflow (e-karyotyping) and greatly…
Follows the expression based karyotyping workflow (e-karyotyping) and greatly simplifies and speeds up the detection analysis of chromosomal aberrations from expression DNA microarrays.
Allows researchers to easily conduct a comprehensive and objective performance…
Allows researchers to easily conduct a comprehensive and objective performance evaluation of their newly developed missing value imputation algorithm for microarray data or any data which can be…
An alternative approach to gene expression estimation that uses a machine…
An alternative approach to gene expression estimation that uses a machine learning approach. MaLTE relies on a gold standard (such as RNA-Seq) to infer gene expression models that make better use of…
Offers powerful yet simple visualization, normalization and significance…
Offers powerful yet simple visualization, normalization and significance testing tools. DetectiV uses simple and well established visualization and statistical techniques to analyze data from…
A simulator of gene expression patterns in order to evaluate different analysis…
A simulator of gene expression patterns in order to evaluate different analysis methods, such as clustering and principle component analysis (PCA).
Uses as submission tool for Microarray experiments. AtMIAMExpress is an…
Uses as submission tool for Microarray experiments. AtMIAMExpress is an open-source Web-based software application for the submission of Arabidopsis-based microarray data to ArrayExpress. It was…
Provides graphical comparison results between normal and cancer with student…
Provides graphical comparison results between normal and cancer with student t-test statistics. Oncopression is focused on microarray-based gene expression profiles for normal and cancer. This web…
A compliant library for computing principal component analysis on incomplete…
A compliant library for computing principal component analysis on incomplete data sets. pcaMethods combines an expectation maximization approach with a probabilistic model. It also offers methods for…
An open-source, platform-independent software pipeline for two-channel…
An open-source, platform-independent software pipeline for two-channel microarray spot quality control. MASQOT-GUI hosts a set of independent applications for gridding, segmentation, quantification,…
An R package that can be used to automatically detect cell-specific marker…
An R package that can be used to automatically detect cell-specific marker genes (MGs) located on the scatter radii of mixed gene expressions, estimate cellular proportions in each sample and…
Allows to generate two conditions biological synthetic microarray dataset with…
Allows to generate two conditions biological synthetic microarray dataset with known characteristics. madsim is a flexible microarray data simulation model where user provides a subset of parameters.…
A fast and flexible delimitation of the most interesting areas in a microarray…
A fast and flexible delimitation of the most interesting areas in a microarray experiment. GiGA identifies all relevant physiological processes, puts them into context, summarizes them in an…
Permits to reconstruct transcriptional regulatory networks. TReNA uses gene…
Permits to reconstruct transcriptional regulatory networks. TReNA uses gene expression, priors, machine learning to process. It is particularly useful in species for which genome-wide transcription…
A statistical method for deconvolving mixed cancer transcriptomes which…
A statistical method for deconvolving mixed cancer transcriptomes which addresses the aforementioned issues in array-based expression data. DeMix can be applied to ongoing biomarker-based clinical…
A meta-analysis method able to efficiently identify associated biomarkers (ABs)…
A meta-analysis method able to efficiently identify associated biomarkers (ABs) from different independently performed array-based datasets. MiningABs quantifies the similarity between paired probe…
A Windows-program for the analysis of experiments with hierarchical probe-sets.…
A Windows-program for the analysis of experiments with hierarchical probe-sets. PhylochipAnalyzer operates in two modes: first, the hierarchy of probes is defined interactively; second, the intensity…
Provides an environment for analyzing both transcriptome data (gene expression…
Provides an environment for analyzing both transcriptome data (gene expression profiles) and metabolome data (compound profiles). KegArray is a Java application that enables users to easily map those…
Estimates missing values for microarray data. KNNimpute provides accurate…
Estimates missing values for microarray data. KNNimpute provides accurate estimation for missing values in genes that belong to small tight expression clusters.
Allows the user to convert id lists in order to unify heterogeneous gene sets.…
Allows the user to convert id lists in order to unify heterogeneous gene sets. MADGene is a software environment comprising a web-based database and a java application. This database creates bridges…
Retrieves data from different microarray databases using MAGE-ML and for…
Retrieves data from different microarray databases using MAGE-ML and for combining microarray data with breast cancer image analysis and clinical data for correlation studies. MAGE-ML provides the…
A collection of functional gene modules calculated from the microarray data…
A collection of functional gene modules calculated from the microarray data compendium available from the GEO database. HCNet is a specialized database designed to assist experimentalists for cardiac…
A tool to compute the number of samples needed to detect expression changes for…
A tool to compute the number of samples needed to detect expression changes for a microarray experiment.
Guides users through the microarray process from RNA procurement to data…
Guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results.
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