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

Software for power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.

Proper citation: CSSP (RRID:SCR_012932) Copy   

•   Source: SciCrunch Registry

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

Software package that provides functions to identify genomic regions of interest based on segmented copy number data from multiple samples.

Proper citation: cghMCR (RRID:SCR_012898) Copy   

•   Source: SciCrunch Registry

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

Software using a non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp).

Proper citation: RankProd (RRID:SCR_013046) Copy   

•   Source: SciCrunch Registry

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

Software developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq).

Proper citation: MEDIPS (RRID:SCR_012996) Copy   

•   Source: SciCrunch Registry

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

Software providing a fast scatterplot smoother suitable for microarray normalization based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.

Proper citation: TurboNorm (RRID:SCR_012963) Copy   

•   Source: SciCrunch Registry

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

Software package that facilitates the primary analysis of ChIP-chip data.

Proper citation: Ringo (RRID:SCR_012973) Copy   

•   Source: SciCrunch Registry

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

Software for handling and analysis of high-throughput microbiome census data.

Proper citation: phyloseq (RRID:SCR_013080) Copy   

•   Source: SciCrunch Registry

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

Software package that is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.

Proper citation: BayesPeak (RRID:SCR_013011) Copy   

•   Source: SciCrunch Registry

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

Software that identifies protein binding sites from ChIP-seq and nucleosome positioning experiments.

Proper citation: ChIPseqR (RRID:SCR_013016) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.6/bioc/html/DEGseq.html

R package to identify differentially expressed genes from RNA-Seq data.

Proper citation: DEGseq (RRID:SCR_008480) Copy   

•   Source: SciCrunch Registry

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

Software tools for quality control, visualization and processing for High-Throughput Sequencing data. These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.

Proper citation: htSeqTools (RRID:SCR_006614) Copy   

•   Source: SciCrunch Registry

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

An R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.

Proper citation: DeconRNASeq (RRID:SCR_006713) Copy   

•   Source: SciCrunch Registry

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

Software package that allows the visualization of DNA methylation data after bisulfite sequencing.

Proper citation: methVisual (RRID:SCR_006705) Copy   

•   Source: SciCrunch Registry

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

Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.

Proper citation: seqbias (RRID:SCR_006832) Copy   

•   Source: SciCrunch Registry

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

Software for merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework.

Proper citation: flowMerge (RRID:SCR_002224) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/2.11/bioc/html/flowPhyto.html

An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.

Proper citation: flowPhyto (RRID:SCR_002183) Copy   

•   Source: SciCrunch Registry

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

Software that implements all bioinformatics steps required for the quantitative, high-resolution analysis of DNA methylation patterns from bisulfite sequencing data.

Proper citation: BEAT (RRID:SCR_002387) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.

Proper citation: CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) Copy   

•   Source: SciCrunch Registry

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

Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

Proper citation: MethylAid (RRID:SCR_002659) Copy   

•   Source: SciCrunch Registry

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

Software for normalization and centralization of array comparative genomic hybridization (aCGH) data with imbalanced aberrations. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).

Proper citation: CGHnormaliter (RRID:SCR_002936) Copy   

•   Source: SciCrunch Registry