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http://bioconductor.org/packages/2.12/bioc/html/Clonality.html

Software package for clonality testing providing statistical tests for clonality versus independence of tumors from the same patient based on their loss of heterozygosity (LOH) or genomewide copy number profiles.

Proper citation: Clonality (RRID:SCR_000293) Copy   

•   Source: SciCrunch Registry

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

Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently.

Proper citation: iBMQ (RRID:SCR_000481) Copy   

•   Source: SciCrunch Registry

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

An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.

Proper citation: GeneExpressionSignature (RRID:SCR_000455) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for flow cytometry data.

Proper citation: flowQ (RRID:SCR_000575) Copy   

•   Source: SciCrunch Registry

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

Algorithm for testing significance of clustering in RNA-seq data.

Proper citation: SigFuge (RRID:SCR_000444) Copy   

•   Source: SciCrunch Registry

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/Starr.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software R package for the analysis of ChIP-chip data and Affymetrix tiling arrays. It provides functions for data import, quality assessment, and data visualization. The software provides tools for the efficient mapping of genomic sequences.

Proper citation: Starr (RRID:SCR_001071) Copy   

•   Source: SciCrunch Registry

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

R software package that uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.

Proper citation: BAC (RRID:SCR_001067) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/data/annotation/html/targetscan.Hs.eg.db.html

R software that predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA.

Proper citation: targetscan.Hs.eg.db (RRID:SCR_001068) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/rGADEM.html

R package with tools for de novo motif discovery in large-scale genomic sequence data.

Proper citation: rGADEM (RRID:SCR_001091) 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/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://rdrr.io/bioc/spotSegmentation/

Model-based software package for processing microarray images so as to estimate foreground and background intensities. The method starts with a very simple but effective automatic gridding method, and then proceeds in two steps. The first step applies model-based clustering to the distribution of pixel intensities, using the Bayesian Information Criterion (BIC) to choose the number of groups up to a maximum of three. The second step is spatial, finding the large spatially connected components in each cluster of pixels. The method thus combines the strengths of the histogram-based and spatial approaches. It deals effectively with inner holes in spots and with artifacts. It also provides a formal inferential basis for deciding when the spot is blank, namely when the BIC favors one group over two or three.

Proper citation: spotSegmentation (RRID:SCR_001298) 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/GeneMeta.html

Software package providing a collection of meta-analysis tools for analysing high throughput experimental data.

Proper citation: GeneMeta (RRID:SCR_001201) 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/ArrayExpress.html

Software to access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

Proper citation: ArrayExpress (R) (RRID:SCR_000120) Copy   

•   Source: SciCrunch Registry

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

Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

Proper citation: AffyRNADegradation (RRID:SCR_000118) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/VariantAnnotation.html

Software package to annotate variants, compute amino acid coding changes, and predict coding outcomes.

Proper citation: VariantAnnotation (RRID:SCR_000074) Copy   

•   Source: SciCrunch Registry