limma - Linear Models for Microarray and Omics Data

Data analysis, linear models and differential expression for omics data.

Last updated 4 days ago

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13.84 score 587 dependents 16k scripts 60k downloads

statmod - Statistical Modeling

A collection of algorithms and functions to aid statistical modeling. Includes limiting dilution analysis (aka ELDA), growth curve comparisons, mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Also includes advanced generalized linear model functions including Tweedie and Digamma distributional families, secure convergence and exact distributional calculations for unit deviances.

Last updated 2 years ago

fortran

9.62 score 1 stars 849 dependents 2.2k scripts 76k downloads

limmaGUI - GUI for limma Package With Two Color Microarrays

A Graphical User Interface for differential expression analysis of two-color microarray data using the limma package.

Last updated 5 months ago

guigeneexpressiondifferentialexpressiondataimportbayesianregressiontimecoursemicroarraymrnamicroarraytwochannelbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrol

4.60 score 1 scripts 361 downloads

affylmGUI - GUI for limma Package with Affymetrix Microarrays

A Graphical User Interface (GUI) for analysis of Affymetrix microarray gene expression data using the affy and limma packages.

Last updated 5 months ago

guigeneexpressiontranscriptiondifferentialexpressiondataimportbayesianregressiontimecoursemicroarraymrnamicroarrayonechannelproprietaryplatformsbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrol

4.60 score 3 scripts 491 downloads

limpa - Quantification and Differential Analysis of Proteomics Data

Quantification and differential analysis of mass-spectrometry proteomics data, with probabilistic recovery of information from missing values. Estimates the detection probability curve (DPC), which relates the probability of successful detection to the underlying expression level of each peptide, and uses it to incorporate peptide missing values into protein quantification and into subsequent differential expression analyses. The package produces objects suitable for downstream analysis in limma. The package accepts peptide-level data with missing values and produces complete protein quantifications without missing values. The uncertainty introduced by missing value imputation is propagated through to the limma analyses using variance modeling and precision weights. The package name "limpa" is an acronym for "Linear Models for Proteomics Data".

Last updated 8 days ago

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3.85 score 6 downloads

dglm - Double Generalized Linear Models

Model fitting and evaluation tools for double generalized linear models (DGLMs). This class of models uses one generalized linear model (GLM) to fit the specified response and a second GLM to fit the deviance of the first model.

Last updated 1 years ago

3.63 score 2 stars 1 dependents 71 scripts 421 downloads