limma - Linear Models for Microarray and Omics Data
Data analysis, linear models and differential expression for omics data.
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exonarraygeneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentdataimportbayesianclusteringregressiontimecoursemicroarraymicrornaarraymrnamicroarrayonechannelproprietaryplatformstwochannelsequencingrnaseqbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrolbiomedicalinformaticscellbiologycheminformaticsepigeneticsfunctionalgenomicsgeneticsimmunooncologymetabolomicsproteomicssystemsbiologytranscriptomicsopenblasopenmp
14.09 score 730 dependents 27k scripts 86k downloadsstatmod - 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.
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10.87 score 1 stars 947 dependents 7.1k scripts 184k downloadsdiffHic - Differential Analysis of Hi-C Data
Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.
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multiplecomparisonpreprocessingsequencingcoveragealignmentnormalizationclusteringhiccurlbzip2xz-utilszlibcpp
6.86 score 2 dependents 60 scripts 773 downloadslimpa - Quantification and Differential Analysis of Proteomics Data
Quantification and differential analysis of mass-spectrometry proteomics data, with probabilistic recovery of information from missing values. Avoids the need for imputation. Estimates the detection probability curve (DPC), which relates the probability of successful detection to the underlying log-intensity of each precursor ion, and uses it to incorporate missing values into protein quantification and into subsequent differential expression analyses. The package produces objects suitable for downstream analysis in limma. The package accepts precursor (or peptide) intensities including missing values and produces complete protein quantifications without the need for imputation. The uncertainty of the protein quantifications is propagated through to the limma analyses using variance modeling and precision weights, ensuring accurate error rate control. The analysis pipeline can alternatively work with PTM or protein level data. The package name "limpa" is an acronym for "Linear Models for Proteomics Data".
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bayesianbiologicalquestiondataimportdifferentialexpressiongeneexpressionmassspectrometrypreprocessingproteomicsregressionsoftwaredifferential-expressionmass-spectrometry
6.24 score 24 stars 45 scripts 428 downloadslimmaGUI - 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.
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guigeneexpressiondifferentialexpressiondataimportbayesianregressiontimecoursemicroarraymrnamicroarraytwochannelbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrol
4.60 score 6 scripts 660 downloadsaffylmGUI - 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.
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guigeneexpressiontranscriptiondifferentialexpressiondataimportbayesianregressiontimecoursemicroarraymrnamicroarrayonechannelproprietaryplatformsbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrol
4.60 score 8 scripts 730 downloadsdglm - 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.
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3.70 score 2 stars 1 dependents 84 scripts 397 downloads