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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

http://www.bioconductor.org/packages/2.13/bioc/html/BeadDataPackR.html

Software that provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.

Proper citation: BeadDataPackR (RRID:SCR_001310) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/OLIN.html

Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data.

Proper citation: OLIN (RRID:SCR_001304) Copy   

•   Source: SciCrunch Registry

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

Software package that provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.

Proper citation: Simpleaffy (RRID:SCR_001302) Copy   

•   Source: SciCrunch Registry

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

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.

Proper citation: qcmetrics (RRID:SCR_001303) Copy   

•   Source: SciCrunch Registry

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

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.

Proper citation: DEXUS (RRID:SCR_001309) Copy   

•   Source: SciCrunch Registry

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

Software for phenotyping Flow Cytometry assays using multidimentional expansion of single dimentional partitions.

Proper citation: flowType (RRID:SCR_001957) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ADaCGH2.html

Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

Proper citation: ADaCGH2 (RRID:SCR_001981) Copy   

•   Source: SciCrunch Registry

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

An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.

Proper citation: TEQC (RRID:SCR_001943) Copy   

•   Source: SciCrunch Registry

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

Software that provides visualization tools for flow cytometry data.

Proper citation: flowViz (RRID:SCR_002075) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.11/bioc/html/flowQB.html

A fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.

Proper citation: flowQB (RRID:SCR_002144) Copy   

•   Source: SciCrunch Registry