Tools   Select Another Resource Report Type

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

Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package.

Proper citation: flowStats (RRID:SCR_000399) Copy   

•   Source: SciCrunch Registry

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/OLINgui.html

Software package providing a graphical user interface for the OLIN package.

Proper citation: OLINgui (RRID:SCR_000435) 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/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

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/ncdfFlow.html

Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data.

Proper citation: ncdfFlow (RRID:SCR_000009) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.

Proper citation: CorMut (RRID:SCR_000053) Copy   

•   Source: SciCrunch Registry

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

A software package to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them. It establishes common bins across tubes in terms of the common markers, then determines expression within each tube for each bin in terms of the tube-specific markers.

Proper citation: flowBin (RRID:SCR_000051) 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://www.fhcrc.org/

Fred Hutchinson Cancer Research Center and Seattle Cancer Care Alliance (SCCA) have merged to form Fred Hutchinson Cancer Center, unified adult cancer research and care center. Independent, nonprofit organization is clinically integrated part of UW Medicine and is UW Medicine’s cancer program.

Proper citation: Fred Hutchinson Cancer Center (RRID:SCR_004984) Copy   

•   Source: SciCrunch Registry

http://master.bioconductor.org/packages/2.13/bioc/html/BHC.html

Software package that performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data and also includes a randomised algorithm which is more efficient for larger data sets.

Proper citation: BHC (RRID:SCR_006399) Copy   

•   Source: SciCrunch Registry

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

Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner.

Proper citation: GSVA (RRID:SCR_021058) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/SimFFPE/

Software R package to simulate artifact chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissue. Simulates normal reads as well as artifact chimeric reads that are enriched in FFPE samples. These artifact chimeric reads can lead to large amounts of false positive structural variant calls.

Proper citation: SimFFPE (RRID:SCR_021085) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/PhenStat.html

Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.

Proper citation: PhenStat (RRID:SCR_021317) Copy   

•   Source: SciCrunch Registry