Tools   Select Another Resource Report Type

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software package developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount.

Proper citation: ExomePeak (RRID:SCR_001076) Copy   

•   Source: SciCrunch Registry

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

Software package that facilitates comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

Proper citation: flowWorkspace (RRID:SCR_001155) Copy   

•   Source: SciCrunch Registry

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

Software package that selects genes associated with survival.

Proper citation: rbsurv (RRID:SCR_001175) Copy   

•   Source: SciCrunch Registry

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

Software package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

Proper citation: ARRmNormalization (RRID:SCR_001292) Copy   

•   Source: SciCrunch Registry

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

Software package to detect different methylation levels (DMR) that gives the exact p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison.

Proper citation: methylMnM (RRID:SCR_001289) 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/iterativeBMAsurv.html

Software package providing a variable selection method for applying survival analysis to microarray data.

Proper citation: iterativeBMAsurv (RRID:SCR_001254) Copy   

•   Source: SciCrunch Registry

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

Software for classes and statistical methods for large single nucleotide polymorphism (SNP) association studies.

Proper citation: snpStats: SnpMatrix and XSnpMatrix classes and methods (RRID:SCR_001249) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages//2.12/bioc/html/exomeCopy.html

Software package for detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

Proper citation: exomeCopy (RRID:SCR_001276) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.14/bioc/html/SMAP.html

Software package providing functions and classes for DNA copy number profiling of array-CGH data.

Proper citation: SMAP (RRID:SCR_001270) Copy   

•   Source: SciCrunch Registry

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

Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages.

Proper citation: wateRmelon (RRID:SCR_001296) 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

http://itb.biologie.hu-berlin.de/~futschik/software/R/cycle/index.html

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

Proper citation: CYCLE (RRID:SCR_001328) 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

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

Software functions for performing print-run and array level quality assessment.

Proper citation: arrayQuality (RRID:SCR_001315) 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/affyPLM.html

Software for fitting probe-level models and tools using these models. Probe-level models (PLM) based quality assessment tools.

Proper citation: affyPLM (RRID:SCR_001319) 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/pvca.html

Software package that contains the function to assess the batch sourcs by fitting all sources as random effects including two-way interaction terms in the Mixed Model (depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book Batch Effects and Noise in Microarray Experiements, chapter 12.

Proper citation: PVCA (RRID:SCR_001356) Copy   

•   Source: SciCrunch Registry