Showing 3 of total 3 results (show query)
bioc
msqrob2:Robust statistical inference for quantitative LC-MS proteomics
msqrob2 provides a robust linear mixed model framework for assessing differential abundance in MS-based Quantitative proteomics experiments. Our workflows can start from raw peptide intensities or summarised protein expression values. The model parameter estimates can be stabilized by ridge regression, empirical Bayes variance estimation and robust M-estimation. msqrob2's hurde workflow can handle missing data without having to rely on hard-to-verify imputation assumptions, and, outcompetes state-of-the-art methods with and without imputation for both high and low missingness. It builds on QFeature infrastructure for quantitative mass spectrometry data to store the model results together with the raw data and preprocessed data.
Maintained by Lieven Clement. Last updated 1 months ago.
proteomicsmassspectrometrydifferentialexpressionmultiplecomparisonregressionexperimentaldesignsoftwareimmunooncologynormalizationtimecoursepreprocessing
11 stars 6.98 score 83 scriptsbioc
satuRn:Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
satuRn provides a higly performant and scalable framework for performing differential transcript usage analyses. The package consists of three main functions. The first function, fitDTU, fits quasi-binomial generalized linear models that model transcript usage in different groups of interest. The second function, testDTU, tests for differential usage of transcripts between groups of interest. Finally, plotDTU visualizes the usage profiles of transcripts in groups of interest.
Maintained by Jeroen Gilis. Last updated 5 months ago.
regressionexperimentaldesigndifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization
21 stars 6.97 score 74 scripts 1 dependents
filipecampelo
tkRplotR:Display Resizable Plots
Display a plot in a Tk canvas.
Maintained by Filipe Campelo. Last updated 4 years ago.
2.18 score 6 scripts 5 dependents