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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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://www.sysbio.se/piano/

Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses.

Proper citation: Piano (RRID:SCR_003200) Copy   

•   Source: SciCrunch Registry
  

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

Software package providing an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. It requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The package implements a pipeline to collect, analyze and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.

Proper citation: ddCt (RRID:SCR_003396) Copy   

•   Source: SciCrunch Registry
  

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

An R package for extending the grammar of graphics for genomic data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

Proper citation: ggbio (RRID:SCR_003313) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/devel/bioc/html/OmicCircos.html

An R software application and package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns.

Proper citation: OmicCircos (RRID:SCR_003292) Copy   

•   Source: SciCrunch Registry
  

http://bioinf.wehi.edu.au/limma/

Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.

Proper citation: LIMMA (RRID:SCR_010943) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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

R functions for the normalization of Exiqon miRNA array data.

Proper citation: ExiMiR (RRID:SCR_012753) Copy   

•   Source: SciCrunch Registry
  

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

Software tools for discriminative motif discovery using regression methods.

Proper citation: motifRG (RRID:SCR_012602) Copy   

•   Source: SciCrunch Registry
  

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

Software package that contains functions for inference of target gene regulation by miRNA, based on only target gene expression profile.

Proper citation: MiRaGE (RRID:SCR_012738) Copy   

•   Source: SciCrunch Registry
  

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

Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Proper citation: DEXSeq (RRID:SCR_012823) Copy   

•   Source: SciCrunch Registry
  

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

Software for strand specific peak-pair calling in ChIP-exo replicates.

Proper citation: CexoR (RRID:SCR_012769) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/edgeR/

Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.

Proper citation: edgeR (RRID:SCR_012802) Copy   

•   Source: SciCrunch Registry
  

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

A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data.

Proper citation: DNaseR (RRID:SCR_012819) Copy   

•   Source: SciCrunch Registry
  

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

Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression, using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR.

Proper citation: tRanslatome (RRID:SCR_012810) Copy   

•   Source: SciCrunch Registry