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http://www.bioconductor.org/packages/release/bioc/html/RchyOptimyx.html
Software that constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response).
Proper citation: RchyOptimyx (RRID:SCR_001889) Copy
http://www.bioconductor.org/packages/2.13/bioc/html/cqn.html
A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.
Proper citation: CQN (RRID:SCR_001786) Copy
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
http://www.bioconductor.org/packages/release/bioc/html/flowType.html
Software for phenotyping Flow Cytometry assays using multidimentional expansion of single dimentional partitions.
Proper citation: flowType (RRID:SCR_001957) Copy
http://www.bioconductor.org/packages/release/bioc/html/ADaCGH2.html
Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.
Proper citation: ADaCGH2 (RRID:SCR_001981) Copy
http://www.bioconductor.org/packages/release/bioc/html/TEQC.html
An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.
Proper citation: TEQC (RRID:SCR_001943) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowViz.html
Software that provides visualization tools for flow cytometry data.
Proper citation: flowViz (RRID:SCR_002075) Copy
https://www.bioconductor.org/packages//2.11/bioc/html/flowQB.html
A fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.
Proper citation: flowQB (RRID:SCR_002144) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowFit.html
A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.
Proper citation: flowFit (RRID:SCR_002286) Copy
http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html
An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
Proper citation: spliceR (RRID:SCR_002280) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowPlots.html
Software for analysis plots and data class for gated flow cytometry data.
Proper citation: flowPlots (RRID:SCR_002177) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowCore.html
A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions.
Proper citation: flowCore (RRID:SCR_002205) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowBeads.html
Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization.
Proper citation: flowBeads (RRID:SCR_002440) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowCyBar.html
A software package to analyze flow cytometric data using gate information to follow population / community dynamics.
Proper citation: flowCyBar (RRID:SCR_002319) Copy
http://www.bioconductor.org/packages/release/bioc/html/ReQON.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.
Proper citation: ReQON (RRID:SCR_000075) Copy
http://www.bioconductor.org/packages/2.13/bioc/html/GenomicRanges.html
Software package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.
Proper citation: GenomicRanges (RRID:SCR_000025) Copy
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
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
http://www.bioconductor.org/packages/2.12/bioc/html/PING.html
Software program for probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.
Proper citation: PING (RRID:SCR_005394) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/DNAcopy.html
Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.
Proper citation: DNAcopy (RRID:SCR_012560) Copy
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