Tools   Select Another Resource Report Type

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations.

Proper citation: flowCL (RRID:SCR_000046) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html

Software package for various databases of microRNA Targets.

Proper citation: RmiR.Hs.miRNA (RRID:SCR_000101) Copy   

•   Source: SciCrunch Registry

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

Software package that fits heterogeneous error models for analysis of microarray data

Proper citation: HEM (RRID:SCR_000194) Copy   

•   Source: SciCrunch Registry

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

Software that establishes a bridge between GEO and BioConductor.

Proper citation: GEOquery (RRID:SCR_000146) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.

Proper citation: MIMOSA (RRID:SCR_000184) Copy   

•   Source: SciCrunch Registry

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

Software for analysis of array CGH data: detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

Proper citation: GLAD (RRID:SCR_001284) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/FilterFFPE/

Software R package to find and filter artificial chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissues. These artificial chimeric reads can lead to large number of false positive structural variant calls. Artifact chimeric read filter to improve SV detection in FFPE samples.

Proper citation: FilterFFPE (RRID:SCR_021086) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/bsseq.html

R package with tools for analyzing and visualizing bisulfite sequencing data.

Proper citation: bsseq (RRID:SCR_001072) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software R package written for analysis of murine palate miRNA two-color expression data.

Proper citation: MmPalateMiRNA (RRID:SCR_001070) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.10/bioc/html/R453Plus1Toolbox.html

R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided.

Proper citation: R453Plus1Toolbox (RRID:SCR_001105) Copy   

•   Source: SciCrunch Registry

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

R package that contains functions to merge microRNA and respective targets using different databases.

Proper citation: RmiR (RRID:SCR_001069) Copy   

•   Source: SciCrunch Registry

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

Software R package for analysis of case-control studies in genetic epidemiology.

Proper citation: CGEN (RRID:SCR_001251) Copy   

•   Source: SciCrunch Registry

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

R software that detects enriched regions of ChIP-seq data sets jointly.

Proper citation: Jmosaics (RRID:SCR_001094) Copy   

•   Source: SciCrunch Registry

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

Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data.

Proper citation: GenoSet (RRID:SCR_001275) Copy   

•   Source: SciCrunch Registry

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

Software package that contains functions and classes that are needed by arrayCGH packages.

Proper citation: CGHbase (RRID:SCR_001279) Copy   

•   Source: SciCrunch Registry

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

Software package that provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.

Proper citation: Simpleaffy (RRID:SCR_001302) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.4/bioc/html/rMAT.html

Software package for normalizing and analyzing tiling arrays and ChIP-chip data. It is the R-version of a MAT program.

Proper citation: rMAT (RRID:SCR_001583) Copy   

•   Source: SciCrunch Registry

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

Software that calls aberrations for array CGH data using a six state mixture model and several biological concepts. It is written in R.

Proper citation: CGHcall (RRID:SCR_001578) Copy   

•   Source: SciCrunch Registry

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

An analysis and visualization software tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes.

Proper citation: SPADE (RRID:SCR_001810) Copy   

•   Source: SciCrunch Registry

http://www.geneontology.org/

Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.

Proper citation: Gene Ontology (RRID:SCR_002811) Copy   

•   Source: SciCrunch Registry