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

A regression based software package to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments.

Proper citation: maSigPro (RRID:SCR_001349) Copy   

•   Source: SciCrunch Registry

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

An easy to use software tool for dual color microarray data. Its GUI-Tk based environment lets any non-experienced user perform a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.

Proper citation: genArise (RRID:SCR_001346) Copy   

•   Source: SciCrunch Registry

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

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.

Proper citation: Harshlight (RRID:SCR_001340) Copy   

•   Source: SciCrunch Registry

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

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.

Proper citation: MiChip (RRID:SCR_001341) Copy   

•   Source: SciCrunch Registry

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

Preprocessing and analysis software for single microarrays and microarray batches.

Proper citation: fRMA (RRID:SCR_001345) Copy   

•   Source: SciCrunch Registry

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

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.

Proper citation: arrayQualityMetrics (RRID:SCR_001335) Copy   

•   Source: SciCrunch Registry

https://rdrr.io/bioc/DEDS/

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.

Proper citation: DEDS (RRID:SCR_001339) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages//2.13/bioc/html/virtualArray.html

Software package that permits the user to combine raw data of different microarray platforms into one virtual array. It consists of several functions that act subsequently in a semi-automatic way. Doing as much of the data combination and letting the user concentrate on analyzing the resulting virtual array.

Proper citation: virtualArray (RRID:SCR_001361) Copy   

•   Source: SciCrunch Registry

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

Software for stepwise normalization functions for cDNA microarray data.

Proper citation: stepNorm (RRID:SCR_001359) Copy   

•   Source: SciCrunch Registry

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

Software package for robust estimation of cDNA microarray intensities with replicates. It uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance.

Proper citation: RAMA (RRID:SCR_001358) Copy   

•   Source: SciCrunch Registry

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

Software packqge for importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH (Comparative genomic hybridization) experiments.

Proper citation: MANOR (RRID:SCR_001305) Copy   

•   Source: SciCrunch Registry

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

Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias.

Proper citation: dyebias (RRID:SCR_001308) Copy   

•   Source: SciCrunch Registry

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

Software package for a Graphical User Interface for the limma Microarray package.

Proper citation: limmaGUI (RRID:SCR_001306) Copy   

•   Source: SciCrunch Registry

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

Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

Proper citation: ffpe (RRID:SCR_001307) Copy   

•   Source: SciCrunch Registry

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

Software package that uses signal-to-noise ratios (SNRs) as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set.

Proper citation: SNAGEE (RRID:SCR_001301) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/CNTools.html

Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.

Proper citation: CNTools (RRID:SCR_000281) Copy   

•   Source: SciCrunch Registry

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

Software package to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.

Proper citation: TransView (RRID:SCR_000358) Copy   

•   Source: SciCrunch Registry

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

Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).

Proper citation: pvac (RRID:SCR_000359) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.

Proper citation: flowFlowJo (RRID:SCR_000410) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/cn.farms.html

Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff.

Proper citation: cn.FARMS (RRID:SCR_000289) Copy   

•   Source: SciCrunch Registry