Tools   Select Another Resource Report Type

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//2.10/bioc/html/aCGH.html

Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.

Proper citation: aCGH (RRID:SCR_013232) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.1/bioc/html/arrayMagic.html

Software providing a collection of utilities for quality control and processing of two-colour cDNA microarray data

Proper citation: arrayMagic (RRID:SCR_010933) Copy   

•   Source: SciCrunch Registry

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

Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data.

Proper citation: NormqPCR (RRID:SCR_003388) Copy   

•   Source: SciCrunch Registry

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

Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package.

Proper citation: SWAN (RRID:SCR_003455) Copy   

•   Source: SciCrunch Registry

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

An R / bioconductor package for detecting similarity in ordered gene lists. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.

Proper citation: OrderedList (RRID:SCR_001834) Copy   

•   Source: SciCrunch Registry

http://www.r-project.org/

Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.

Proper citation: R Project for Statistical Computing (RRID:SCR_001905) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor software package for automated gating of flow cytometry data that implements a robust model-based clustering approach based on multivariate t mixture models with the Box-Cox transformation.

Proper citation: flowClust (RRID:SCR_001807) Copy   

•   Source: SciCrunch Registry

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

Software for combinatorial polyfunctionality analysis of single cells. It is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. It uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.

Proper citation: COMPASS (RRID:SCR_001801) Copy   

•   Source: SciCrunch Registry

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

Software that provides utilities for flow cytometry data.

Proper citation: flowUtils (RRID:SCR_001879) Copy   

•   Source: SciCrunch Registry

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

Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations.

Proper citation: flowTrans (RRID:SCR_002093) Copy   

•   Source: SciCrunch Registry

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

Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process.

Proper citation: flowMap (RRID:SCR_002269) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.13/bioc/html/shinyTANDEM.html

Software package that provides a GUI interface for rTANDEM, an R/Bioconductor package for MS/MS protein identification. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it will also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files.

Proper citation: shinyTANDEM (RRID:SCR_002169) Copy   

•   Source: SciCrunch Registry

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

Software for matching cell populations and building meta-clusters and templates from a collection of flow cytometry (FC) samples.

Proper citation: flowMatch (RRID:SCR_002283) Copy   

•   Source: SciCrunch Registry