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http://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html

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

Proper citation: SCAN.UPC (RRID:SCR_001334) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/snm.html

Software package that uses a modeling strategy especially designed for normalizing high-throughput genomic data. The premise is that your data is a function of study-specific variables which are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.

Proper citation: SNM (RRID:SCR_001299) Copy   

•   Source: SciCrunch Registry

https://rdrr.io/bioc/betr/man/betr.html#heading-0

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

Proper citation: betr (RRID:SCR_001332) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages//2.11/bioc/html/gprege.html

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).

Proper citation: gprege (RRID:SCR_001324) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.13/bioc/html/waveTiling.html

Software package to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.

Proper citation: waveTiling (RRID:SCR_001322) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/AffyExpress.html

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.

Proper citation: AffyExpress (RRID:SCR_001321) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/beadarray.html

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.

Proper citation: beadarray (RRID:SCR_001314) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/arrayMvout.html

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.

Proper citation: arrayMvout (RRID:SCR_001317) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.7/bioc/html/affyQCReport.html

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.

Proper citation: affyQCReport (RRID:SCR_001318) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.12/bioc/html/maigesPack.html

Software package that uses functions to handle and analyze cDNA microarray data.

Proper citation: maigesPack (RRID:SCR_001351) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/mdqc.html

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.

Proper citation: MDQC (RRID:SCR_001352) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/macat.html

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.

Proper citation: MACAT (RRID:SCR_001350) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/nnNorm.html

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.

Proper citation: nnNorm (RRID:SCR_001354) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/maCorrPlot.html

Software that graphically displays correlation in microarray data that is due to insufficient normalization.

Proper citation: maCorrPlot (RRID:SCR_001348) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/lapmix.html

Software to identify differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes.

Proper citation: lapmix (RRID:SCR_001347) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/OCplus.html

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).

Proper citation: OCplus (RRID:SCR_001342) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages//2.11/bioc/html/bridge.html

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.

Proper citation: bridge (RRID:SCR_001343) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.12/bioc/html/CALIB.html

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.

Proper citation: CALIB (RRID:SCR_001338) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/LPE.html

Software library used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional "BH" or "BY" procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions.

Proper citation: LPE (RRID:SCR_001364) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/aroma.light.html

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.

Proper citation: aroma.light (RRID:SCR_001312) Copy   

•   Source: SciCrunch Registry