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

Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.

Proper citation: RUVSeq (RRID:SCR_006263) Copy   

•   Source: SciCrunch Registry

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

An R / bioconductor package for detecting similarity in ordered gene lists. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.

Proper citation: OrderedList (RRID:SCR_001834) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.

Proper citation: metahdep (RRID:SCR_001225) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. R extension whose functions are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be "list", "matrix", or "ExpressionSet". The main function is "mergeExprs" which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function "intcor" calculate the correlation coefficients. Other functions use the output from "modelOutcome" to graphically display the results and cross-validate associations of gene expression data with survival.

Proper citation: MergeMaid (RRID:SCR_001221) Copy   

•   Source: SciCrunch Registry

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

A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

Proper citation: globaltest (RRID:SCR_001256) Copy   

•   Source: SciCrunch Registry

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

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.

Proper citation: factDesign (RRID:SCR_001330) Copy   

•   Source: SciCrunch Registry

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

Software for adaptive Gene Picking for Microarray Expression Data Analysis.

Proper citation: pickgene (RRID:SCR_001331) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.10/bioc/html/oneChannelGUI.html

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.

Proper citation: oneChannelGUI (RRID:SCR_001325) Copy   

•   Source: SciCrunch Registry

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

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

Proper citation: LMGene (RRID:SCR_001329) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/affylmGUI/

R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11.

Proper citation: affylmGUI (RRID:SCR_001320) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.10/bioc/html/ArrayTools.html

Software package for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

Proper citation: ArrayTools (RRID:SCR_001313) Copy   

•   Source: SciCrunch Registry

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

Software to detect differential expression in microarray and proteomics datasets. Its use has been shown to improve the detection of differentially expressed genes or proteins in these datasets.

Proper citation: plgem (RRID:SCR_001355) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) and combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform.

Proper citation: metaArray (RRID:SCR_001353) Copy   

•   Source: SciCrunch Registry

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

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

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/timecourse.html

Software functions for data analysis and graphical displays for developmental microarray time course data.

Proper citation: timecourse (RRID:SCR_000077) Copy   

•   Source: SciCrunch Registry

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

Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.

Proper citation: metaSeq (RRID:SCR_000056) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/devel/bioc/html/SeqGSEA.html

Software package that provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene''s differential expression and splicing, respectively.

Proper citation: SeqGSEA (RRID:SCR_005724) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/tweeDEseq.html

Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.

Proper citation: tweeDEseq (RRID:SCR_003038) Copy   

•   Source: SciCrunch Registry