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Statistics for biology software tools | Synthetic biology

fastICA
Desktop

fastICA fast Independent Component Analysis

Provides a batch version of a neural learning algorithm for Independent…

Provides a batch version of a neural learning algorithm for Independent Component Analysis (ICA). fastICA is an R package based on a fixed-point method. It was introduce using a very simple yet…

ROCR
Desktop

ROCR

Allows to evaluate and visualize the performance of scoring classifiers. ROCR…

Allows to evaluate and visualize the performance of scoring classifiers. ROCR features over 25 performance measures that can be freely combined to create two-dimensional performance curves. It uses…

pROC
Desktop

pROC

Contains a set of tools displaying, analyzing, smoothing and comparing receiver…

Contains a set of tools displaying, analyzing, smoothing and comparing receiver operating characteristic (ROC) curves. pROC proposes multiple statistical tests to compare ROC curves, and in…

SGoF
Desktop

SGoF

Fixes the rejection region in multiple hypothesis testing adjustment. SGoF uses…

Fixes the rejection region in multiple hypothesis testing adjustment. SGoF uses a discriminant rule based on the maximum distance between the uniform distribution of p-values and the observed one, to…

VALORATE
Desktop

VALORATE

Estimates the null distribution and the p-value of the log-rank based on a…

Estimates the null distribution and the p-value of the log-rank based on a recent reformulation. VALORATE was developed and tested for cancer genomics that is heavily affected by unbalanced survival…

RAICAR
Desktop

RAICAR Ranking and Averaging Independent Component Analysis by Reproducibility

Improves the decomposition and interpretation of functional magnetic resonance…

Improves the decomposition and interpretation of functional magnetic resonance imaging (fMRI) data with independent component analysis (ICA). RAICAR is an ICA method based on reproducibility. The…

randomforest
Desktop

randomforest

Implements an algorithm for classification and regression. Randomforest…

Implements an algorithm for classification and regression. Randomforest provides an R interface that can also be used in unsupervised mode for assessing proximities among data points. This package…

MIPReSt
Desktop

MIPReSt Mixed ICA/PCA via Reproducibility Stability

Allows to assess component stability as the size of the data matrix changes,…

Allows to assess component stability as the size of the data matrix changes, which can be used to determine the dimension of the non-gaussian subspace in a mixture. MIPReSt is an algorithm for mixed…

chngpt
Desktop

chngpt

Fits thresholded logistic regression models. chngpt supports four variants of…

Fits thresholded logistic regression models. chngpt supports four variants of threshold regression models that are most widely used in practice. It implements both estimation and hypothesis testing…

BICAR
Desktop

BICAR Bidirectional Independent Component Averaged Representation

Allows to obtain robust, reproducible pairs of temporal and spatial components…

Allows to obtain robust, reproducible pairs of temporal and spatial components at the individual subject level from concurrent electroencephalographic and functional magnetic resonance imaging data.…

frailtySurv
Desktop

frailtySurv

Generates clustered survival data under a wide range of conditions thanks to a…

Generates clustered survival data under a wide range of conditions thanks to a set of simulation functions. frailtySurv allows users to simulate and fits semiparametric shared frailty models and is…

BNNPT
Desktop

BNNPT Bagging Nearest-Neighbor Prediction Test

Detects independence between two random variables especially in non-linear…

Detects independence between two random variables especially in non-linear situations. BNNPT is based on a permutation test of the square error (SE) of bagging nearest neighbor estimator. It is able…

STATegRa
Desktop

STATegRa

Offers user-friendly tools for the integration of different omics data types.…

Offers user-friendly tools for the integration of different omics data types. STATegRa focuses on several sequencing based functional genomics methods, proteomics and metabolomics. It provides…

OPATs
Desktop

OPATs Omnibus P-value Association Tests

Permits P-value combinations by using popular analysis methods. OPATs enables a…

Permits P-value combinations by using popular analysis methods. OPATs enables a gene region to be extended upstream and downstream by a prespecified width. It can be used to identify genetic markers…

VARI
Desktop

VARI

Aims to detect and genotype simple and complex genetic variants in an…

Aims to detect and genotype simple and complex genetic variants in an individual or population. VARI is an implementation of a succinct colored de Bruijn graph that significantly reduces the amount…

LTRCtrees
Desktop

LTRCtrees

Proposes two survival trees for left-truncated and right-censored (LTRC) data,…

Proposes two survival trees for left-truncated and right-censored (LTRC) data, which can be seen as a generalization of the traditional survival tree for right-censored data. LTRCrees can be used to…

Stan
Desktop

Stan

Allows users to specify a broad range of models involving continuous parameters…

Allows users to specify a broad range of models involving continuous parameters by coding their log posteriors up to a proportion. Stan is a state-of-the-art platform for statistical modeling and…

FriedmanRSD
Desktop

FriedmanRSD

Determines the exact p-value of the absolute rank sum difference of a pair of…

Determines the exact p-value of the absolute rank sum difference of a pair of Friedman rank sums, making asymptotic tests obsolete. FriedmanRSD calculates the probability mass distribution of the…

MultiwayClassif…
Desktop

MultiwayClassification

Classifies linearly high-dimensional multi-way data, in which coefficients can…

Classifies linearly high-dimensional multi-way data, in which coefficients can be factorized into weights that are specific to each dimension. MultiwayClassification extends existing classification…

SBC
Desktop

SBC Survival-based Bayesian Clustering

Allows users to detect clinically disease subtypes. SBC combines an Accelerated…

Allows users to detect clinically disease subtypes. SBC combines an Accelerated Failure Time (AFT) model coupled to a Dirichlet Process Gaussian Mixture Model (DPMM) to gather clinical end point data…

FANOVA
Desktop

FANOVA Functional ANalysis Of VAriance

Allows discovery of unknown gene functions. FANOVA is based on a Gaussian…

Allows discovery of unknown gene functions. FANOVA is based on a Gaussian process. It can identify significant differential growth between the trajectories of transcription factor (TF) knockouts…

ICAclust
Desktop

ICAclust

Considers jointly Independent Component Analysis (ICA) and a hierarchical…

Considers jointly Independent Component Analysis (ICA) and a hierarchical method for clustering temporal RNA-Seq data. ICAclust methodology present some advantages: (i) the dependence between…

MSA-Enet
Desktop

MSA-Enet Multi-Step Adaptive Elastic-net

Reduce the false positives in high-dimensional variable selection while still…

Reduce the false positives in high-dimensional variable selection while still maintaining the estimation accuracy. MSA-Enet was applied on a high-dimensional variable selection problem of motif…

feseR
Desktop

feseR Feature Selection in R

Helps with bioinformatics machine learning troubles. feseR is an R package for…

Helps with bioinformatics machine learning troubles. feseR is an R package for high-dimensional omics data analysis. With a feature selection, this application provides a workflow combined…

RL-SKAT
Desktop

RL-SKAT Recalibrated Lightweight Sequence Kernel Association Test

Allows exact p-value calculation score test in heritability. RL-SKAT is a…

Allows exact p-value calculation score test in heritability. RL-SKAT is a computational method that can be used in the case of a single variance component and constant response vector. This process…

ACT
Desktop

ACT Aggregation and Correlation Toolbox

Analyzes continuous signal and discrete region tracks from high-throughput…

Analyzes continuous signal and discrete region tracks from high-throughput genomic experiments. ACT is able to generate aggregate profiles of a given track around a set of specified anchor points,…

MINERVA
Desktop
pensim
Desktop

pensim

Predicts the survival of cancer patients from microarray data, and classifies…

Predicts the survival of cancer patients from microarray data, and classifies obese and lean individuals from metagenomic data. pensim can be applied for high-dimensional feature selection and…

G*Power
Desktop

G*Power

Allows a variety of statistical tests. G*Power can analyze the power of tests…

Allows a variety of statistical tests. G*Power can analyze the power of tests based on (1) single-sample tetrachoric correlations, (2) comparisons of dependent correlations, (3) bivariate linear…

LAMP
Desktop

LAMP Limitless-Arity Multiple-testing Procedure

Counts the exact number of “testable” motif combinations and derives a…

Counts the exact number of “testable” motif combinations and derives a tighter bound of family-wise error rate (FWER), allowing the calibration of the Bonferroni factor. LAMP is a…

MSSS
Desktop

MSSS Minimum Sum of Squared Similarities

Allows incremental sampling in Nystrom based-spectral clustering. MSSS is a…

Allows incremental sampling in Nystrom based-spectral clustering. MSSS is a cluster algorithm based on Nystrom method. It starts sampling with a fixed number of initial landmark points and selects…

Quantreg
Desktop

Quantreg Quantile Regression

Provides a set of approaches for conditional quantiles’ models. Quantreg is a…

Provides a set of approaches for conditional quantiles’ models. Quantreg is a package which includes (i) models: linear and nonlinear parametric and non-parametric and (ii) methods for :…

HHG
Desktop

HHG Heller-Heller-Gorfine

Provides a set for evaluating multivariate and univariate k-sample homogeneity…

Provides a set for evaluating multivariate and univariate k-sample homogeneity and independence. HHG is an R package including Heller-Heller-Gorfine ('HHG') statistical tests for…

tdROC
Web
Desktop

tdROC Time Dependent ROC Analysis Tool

Computes receiver operating characteristics (ROC) curve. tdROC is an R module…

Computes receiver operating characteristics (ROC) curve. tdROC is an R module that calculates the time-dependent sensitivity and specificity and area under the curve (AUC) using a nonparametric…

onewaytests
Web
Desktop

onewaytests

Enables to study effects of treatment on a dependent variable. Onewaytests is a…

Enables to study effects of treatment on a dependent variable. Onewaytests is a web-based tool that offers present unidirectional tests in independent groups, pair-wise comparisons, graphical…

easyROC
Web

easyROC easy Receiver Operating Characteristics

Offers a large variety of graphical tools for visual inspection of receiver…

Offers a large variety of graphical tools for visual inspection of receiver operating characteristics (ROC) curves, including ROC curves, sensitivity and specificity curves and distribution plots.…

MVN
Web

MVN MultiVariate Normality

Offers comprehensive flexibility for assessing multivariate normality (MVN)…

Offers comprehensive flexibility for assessing multivariate normality (MVN) assumption. MVN is an R package for multivariate normality checking. This package provides some graphical approaches such…

EXCALIBUR
Desktop

EXCALIBUR

Allows users to compute elicitation by providing various features for analyzing…

Allows users to compute elicitation by providing various features for analyzing and understand the data. Excalibur is a standalone software which provides a platform utilizing Cooke’s Classical…

Elicitator
Desktop

Elicitator

Offers a framework for expert elicitation. Elicitator is an open source…

Offers a framework for expert elicitation. Elicitator is an open source software that aims to extend the interactive dynamic style of elicitation and to be easily interpreted, and suitable for a wide…

GNU MCSim
Desktop

GNU MCSim

Allows creation of statistical or simulation models. GNU MCSim is able to…

Allows creation of statistical or simulation models. GNU MCSim is able to perform a series of simulations along a Markov-chain Monte Carlo (MCMC) in the model parameter space. It can obtain the…

caret
Desktop

caret Classification And REgression Training

Provides a set of functions that attempt to streamline the process for creating…

Provides a set of functions that attempt to streamline the process for creating predictive models. caret is an R package that contains tools for (i) data splitting, (ii) pre-processing, (iii) feature…

PathoStat
Desktop

PathoStat

Allows to work about statistical microbiome analysis on metagenomics results…

Allows to work about statistical microbiome analysis on metagenomics results from sequencing data samples. PathoStat supports analyses on the PathoScope generated by report files. It provides various…

Rsolnp
Desktop

Rsolnp

Uses augmented Lagrange multiplier method for general non-linear optimization.…

Uses augmented Lagrange multiplier method for general non-linear optimization. Rsolnp enables the generation of a set of randomly chosen parameters from which to initialize multiple restarts of the…

G T A T C G C T A
Picard
Desktop

Picard

A set of tools (in Java) for working with next generation sequencing data in…

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

Qvality
Web
Desktop

Qvality

Estimates q-values and posterior error probabilities (PEP) directly from score…

Estimates q-values and posterior error probabilities (PEP) directly from score distributions. Qvality employs a standard bootstrap procedure to estimate the prior probability of a score being from…

minepy
Desktop

minepy

Computes maximal information-based measures of dependence between two variables…

Computes maximal information-based measures of dependence between two variables in large datasets. minepy reduces the large memory requirement of the original Java implementation, has good upscaling…

MATCH
Web

MATCH

Supplies a web application for elicitation and fitting prediction. MATCH is…

Supplies a web application for elicitation and fitting prediction. MATCH is derived from SHELF provides five methods (roulette, quartile, tertile, probability, and hybrid method). The software…

FactoMineR
Desktop

FactoMineR

Allows multivariate data analysis. FactoMineR allows to take into account…

Allows multivariate data analysis. FactoMineR allows to take into account different types of variables (quantitative or categorical), different types of structure on the data (a partition on the…

CircStat
Desktop

CircStat Circular Statistics Toolbox

Provides methods for the descriptive and inferential statistical analysis of…

Provides methods for the descriptive and inferential statistical analysis of directional data. CircStat can be used to explore and summarize important properties of a sample of angular data such as…

DiscoverySpace
Desktop

DiscoverySpace

Assists users in conceptualization, visualization and manipulation of datasets…

Assists users in conceptualization, visualization and manipulation of datasets available on the DiscoveryDB database. DiscoverySpace supports all possible data models with only minimal configuration…

SHELF
Desktop

SHELF SHeffield ELicitation Framework

Provides a method for elicitating probability distributions for uncertain…

Provides a method for elicitating probability distributions for uncertain quantities. SHELF includes several tutorials and a rich documentation for users’ guidance.

PyLESS
Desktop

PyLESS

Allows working on dimension reduction in dynamic models. PyLESS can perform…

Allows working on dimension reduction in dynamic models. PyLESS can perform model reduction on different types of input models given in systems biology markup language (SBML) format or in matrix form.

SokanProject
Desktop

SokanProject

Allows users to calculate Pearson's correlation coefficients.

Allows users to calculate Pearson's correlation coefficients.

OPWeight
Desktop

OPWeight

Performs weighted-p-value based multiple hypothesis test. OPWeight provides…

Performs weighted-p-value based multiple hypothesis test. OPWeight provides corresponding information such as ranking probability, weight, significant tests, and others. The main function of this…

MATLAB
Desktop

MATLAB

Allows to design and analyze different systems. MATLAB is used in several…

Allows to design and analyze different systems. MATLAB is used in several domains as: (1) robotics, (2) computer vision, (3) image processing, (4) machine learning, and more. It permits to apply its…

Interactive…
Desktop

Interactive Platform for Statistical Computing

Allows to perform various statistical computations without having any knowledge…

Allows to perform various statistical computations without having any knowledge of the high-level programming languages. Interactive Platform for Statistical Computing is a web-based platform which…

Wizard
Desktop

Wizard

Makes multivariate data analysis easy and fun. Wizard is a statistics program…

Makes multivariate data analysis easy and fun. Wizard is a statistics program designed to generates only a few kinds of plots (scatterplots, pie charts, histograms) and performs only a handful of…

MorePower
Desktop

MorePower

Computes sample size, effect size, and power statistics for factorial ANOVA…

Computes sample size, effect size, and power statistics for factorial ANOVA designs. MorePower calculates relational confidence intervals for ANOVA effects, as well as Bayesian posterior…

BBR
Desktop

BBR Biostatistics for Biomedical Research

Requires various images that are symbolically linked to subdirectories, a…

Requires various images that are symbolically linked to subdirectories, a bibliographic database, and LaTeX style files.

ROCPLOT
Desktop

ROCPLOT

Performs receiver operating characteristic (ROC) analysis on one or more files…

Performs receiver operating characteristic (ROC) analysis on one or more files of search results. ROCPLOT generates the following: (i) ROC values, giving a convenient numerical measure of method…

CodonStatistics
Desktop

CodonStatistics

Enables to quickly browse statistical information on one or more genomes.…

Enables to quickly browse statistical information on one or more genomes. CodonStatistics is a java based user interface. One may view statistical information on both graphical and tabular forms. The…

AdaptiveGP
Desktop

AdaptiveGP

An implementation of a fully nonstationary, heteroscedastic Gaussian process…

An implementation of a fully nonstationary, heteroscedastic Gaussian process for Matlab. The three key components of a squared exponential kernel are all modeled as functions with separate GP priors.

PERM
Desktop

PERM

Detects statistical connections between grouping structures and grouping…

Detects statistical connections between grouping structures and grouping factors or correlates. PERM takes in a collection of grouped data and outputs a P-value. It allows to compute P-values from…

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