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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.

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• SciCrunch
• 13 years ago - by Anonymous

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).

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• SciCrunch
• 13 years ago - by Anonymous

Software package that takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.

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• SciCrunch
• 13 years ago - by Anonymous

Software package used to detect extended, diffuse and compact blemishes on microarray chips. It automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection.

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• SciCrunch
• 13 years ago - by Anonymous

Software library that contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements methodology (Differential Expression via Distance Summary) which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.

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• SciCrunch
• 13 years ago - by Anonymous

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.

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• SciCrunch
• 13 years ago - by Anonymous

Imagescience provides a database of scientific imaging conferences around the world. Sponsors: This database is supported by imagescience.org.

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• SciCrunch
• 17 years ago - by Anonymous

Web-based resource that provides an integrated set of tools for DNA sequence anlaysis, plasmid map creation, sequence viewing, and various biochemical calculations.

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• SciCrunch
• 15 years ago - by Anonymous

Software package that generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). Reports contain both general and platform-specific sections. Both one and two color array platforms are supported.

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• SciCrunch
• 13 years ago - by Anonymous

A microarray normalization software (SCAN) to facilitate personalized-medicine workflows with an extension (UPC) that estimates whether a given gene/transcript is active above background levels in a given sample. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. A

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• SciCrunch
• 13 years ago - by Anonymous

Software for target enrichment performance for next-generation sequencing.

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• SciCrunch
• 12 years ago - by Anonymous

Software package that implements the Bayesian Estimation of Temporal Regulation algorithm to identify differentially expressed genes in microarray time-course data.

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• SciCrunch
• 13 years ago - by Anonymous

Software for adaptive Gene Picking for Microarray Expression Data Analysis.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.

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• SciCrunch
• 13 years ago - by Anonymous

Software package for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays.

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• SciCrunch
• 13 years ago - by Anonymous

Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models.

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• SciCrunch
• 13 years ago - by Anonymous

Wiki of chemical and preparatory experimental protocols.

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• SciCrunch
• 17 years ago - by Anonymous

A Swiss global health-care company that operates under two divisions: Pharmaceuticals and Diagnostics.

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• SciCrunch
• 14 years ago - by Anonymous

Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code.

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• SciCrunch
• 13 years ago - by Anonymous

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).

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• SciCrunch
• 13 years ago - by Anonymous