Tools   Select Another Resource Report Type

http://cran.r-project.org/web/packages/muma/

Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY).

Proper citation: MUMA (RRID:SCR_002412) Copy   

•   Source: SciCrunch Registry

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

Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.

Proper citation: nondetects (RRID:SCR_001702) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/enviPick/

Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot.

Proper citation: enviPick (RRID:SCR_003059) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor software package for fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.

Proper citation: flowFP (RRID:SCR_001537) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/MCMC.qpcr/

Software package that implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a classic model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results.

Proper citation: MCMC.qpcr (RRID:SCR_001721) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.7/bioc/html/plateCore.html

Software that provides basic S4 data structures and routines for analyzing plate based flow cytometry data.

Proper citation: plateCore (RRID:SCR_001743) Copy   

•   Source: SciCrunch Registry

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

Software functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH.

Proper citation: SLqPCR (RRID:SCR_001669) 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.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://genome.gsc.riken.jp/osc/english/dataresource/

A program to eliminate artifactual reads from next-generation sequencing data sets.

Proper citation: TagDust (RRID:SCR_004175) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/kdetrees/

R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.

Proper citation: Kdetrees (RRID:SCR_004522) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/YuGene/

Software providing a simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison of identical probes. YuGene works on a range of microarray dataset distributions, such as between manufacturers. The resulting output allows direct comparisons of gene expression between experiments and experimental platforms.

Proper citation: YuGene (RRID:SCR_006023) Copy   

•   Source: SciCrunch Registry

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

Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.

Proper citation: RUVSeq (RRID:SCR_006263) Copy   

•   Source: SciCrunch Registry

http://updepla1srv1.epfl.ch/waszaks/absfilter/

R package for identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

Proper citation: ABS filter (RRID:SCR_005328) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/aLFQ/

An R-package for estimating absolute protein quantities from label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics data. It supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, they used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation.

Proper citation: aLFQ (RRID:SCR_005925) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/reseqtools/

A Toolkit for analyzing next-generation DNA Re-Sequencing data.

Proper citation: reseqtools (RRID:SCR_010806) Copy   

•   Source: SciCrunch Registry

https://github.com/AliView

Software for aligning viewing and editing dna / aminiacid sequences, intuitive, fast and leightweight. It has been designed to meet the requirements of next generation sequencing era phylogenetic datasets.

Proper citation: AliView (RRID:SCR_002780) Copy   

•   Source: SciCrunch Registry

https://github.com/ahmohamed/NetPathMiner

Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths.

Proper citation: NetPathMiner (RRID:SCR_002757) Copy   

•   Source: SciCrunch Registry