Software Map

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ANOVA Bayesian Bioinformatics Bioinformatics & Biostatistics Biostatistics C++ Cancer Chemoinformatics Classification Clustering Copynumber DNA Ecology Economics Finance GUI Genetic Algorithms Genetics HTML Machine Learning Machine learning Mixture Multiple Comparisons Multivariate Analysis Multivariate Regression Multivariate Techniques Next generation Sequencing ODE Phylogeny R R-Forge Rcmdr Regression SNP Statistics Time series Visualization Whole-genome bioinformatics biostatistics break detection categorical change detection classification clustering community ecology data mining database datasets dissimilarity distance distributions diversity dynamic systems ecological models ecology econometrics economics epidemiology finance gene expression generalized linear models genetics graphics high dimentional data likelihood linear models machine learning microarray missing data missing values mixed effect models mixed model model comparison model estimation model selection movement multivariate multivariate regression multivariate statistics non-parametrics nonlinear models nonparametric optimization parametric model permutation tests phylogeny plotting political analysis prediction psychology raster regression remote sensing reporting robust robust statistics simulation soil spatial spatial autocorrelation spatial classes spatial data spatial methods spatial point patterns spatial regression spatio-temporal species distribution models stochastic processes survival teaching text mining time series visualization

11 projects in result set.
Benchmarking genomic data integration - Comparison pipeline for multi-platform data integration algorithms for functional genomics studies. Provides tools to compare performance between publicly available implementations
Tags: Bioinformatics, CCA, Cancer, Copynumber, Machine Learning, Machine learning, Multivariate Regression, Normalization, R, R-Forge, Whole-genome, analytics, biostatistics, comparative analysis, comparison, data mining, dependence, gene expression, machine learning, microarray, multivariate

Activity Percentile: 0
Activity Ranking: 0
Registered: 2011-02-02 00:51

CellMix - Resources for performing gene expression deconvolution in R, i.e. estimating cell proportions and/or cell-specific gene expression from global gene expression measured in heterogeneous samples. Currently hosted packages: csSAM and CellMix packages.
Tags: deconvolution, gene expression

Activity Percentile: 0
Activity Ranking: 0
Registered: 2013-04-11 08:27

Class Prediction - A suite of packages that can bu used for "class prediction" problems. Includes tools to standardize training-testing regimens and cross-validation schemes.
Tags: Bioinformatics, Gene expression, Genetic Algorithms, Machine Learning, Machine learning, Multivariate Regression, Self-Organizing Map, bioinformatics, classification, cross-validation, gene expression, genetic algorithms, machine learning, model, prediction, validation

Activity Percentile: 87
Activity Ranking: 9
Registered: 2014-02-03 16:15

HTSAnalysis - This project contains R packages for the statistical analysis of high throughput sequencing data.
Tags: Filter, RNA-seq, Differential expression analysis, Bioinformatics, Next generation Sequencing, gene expression

Activity Percentile: 0
Activity Ranking: 0
Registered: 2012-10-16 20:41

Mixed-pair mutual information estimators - Fast calculation mutual information for comparisons between all types of variables including continuous vs continuous, continuous vs discrete and discrete vs discrete. Also provides jackknife bias correction and tests for association.
Tags: Bioinformatics, categorical, data mining, dependence, dissimilarity, entropy, gene expression, genetics, independence, microarray

Activity Percentile: 0
Activity Ranking: 0
Registered: 2012-08-10 08:48

NewmanOmics - Develop and implement extensions to the Newman studentized range statistic that can be applied to transcriptomic data
Tags: Bioinformatics, Bioinformatics & Biostatistics, bioinformatics, gene expression

Activity Percentile: 0
Activity Ranking: 0
Registered: 2017-02-15 20:58

OOMPA - OOMPA is a suite of R packages for the analysis of gene expression (RNA), proteomics profiling , and other high throughput molecular biology data. OOMPA uses S4 classes to construct object-oriented tools with a consistent user interface.
Tags: Bioinformatics, Clustering, Differential expression analysis, Gene expression, Multiple Comparisons, Multivariate Analysis, bioinformatics, clustering, false discovery rate, gene expression, high dimentional data, microarray, multivariate, permutation tests

Activity Percentile: 95
Activity Ranking: 4
Registered: 2013-08-29 17:48

UMPIRE - UMPIRE provides tools to simulate realistic biological expression data. It includes additive and multiplicative noise, correlated expression, inactive genes, and a link to outcome data that incorporates the multi-hit cancer model.
Tags: Bioinformatics, Cancer, Gene expression, bioinformatics, gene expression, simulation, simulations, synthetic dataset

Activity Percentile: 76
Activity Ranking: 16
Registered: 2014-02-03 16:37

neaGUI - NeaGUI is a user friendly package developed to implement a method of network enrichment analysis (NEA) that extends the overlap statistics in GEA to network links between genes in the experimental set and those in the functional categories.
Tags: network enrichment analysis, microarray, gene expression
This project has not yet categorized itself in the Trove Software Map

Activity Percentile: 0
Activity Ranking: 0
Registered: 2012-03-29 19:40

netbenchmark - The development version of netbenchmark package, which implements a benchmarking of several gene network inference algorithms from gene expression data.
Tags: Gene expression, R, RStudio, Rcpp, benchmark, gene expression, gene networks, Bioinformatics

Activity Percentile: 0
Activity Ranking: 0
Registered: 2014-11-28 09:55

pathview - Pathview is a novel tool set in for pathway based data integration and visualization. It downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway, and renders pathway graph with the mapped data.
Tags: Bioinformatics, Visualization, gene expression, microarray
This project has not yet categorized itself in the Trove Software Map

Activity Percentile: 0
Activity Ranking: 0
Registered: 2013-03-07 22:20

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