topconfects - Top Confident Effect Sizes

Rank results by confident effect sizes, while maintaining False Discovery Rate and False Coverage-statement Rate control. Topconfects is an alternative presentation of TREAT results with improved usability, eliminating p-values and instead providing confidence bounds. The main application is differential gene expression analysis, providing genes ranked in order of confident log2 fold change, but it can be applied to any collection of effect sizes with associated standard errors.

Last updated 24 days ago

geneexpressiondifferentialexpressiontranscriptomicsrnaseqmrnamicroarrayregressionmultiplecomparison

7.26 score 14 stars 2 packages 18 scripts 292 downloads

langevitour - Langevin Tour

An HTML widget that randomly tours 2D projections of numerical data. A random walk through projections of the data is shown. The user can manipulate the plot to use specified axes, or turn on Guided Tour mode to find an informative projection of the data. Groups within the data can be hidden or shown, as can particular axes. Points can be brushed, and the selection can be linked to other widgets using crosstalk. The underlying method to produce the random walk and projection pursuit uses Langevin dynamics. The widget can be used from within R, or included in a self-contained R Markdown or Quarto document or presentation, or used in a Shiny app.

Last updated 3 months ago

javascript-applicationslangevin-dynamicstourvisualization

6.74 score 25 stars 1 packages 21 scripts 602 downloads

weitrix - Tools for matrices with precision weights, test and explore weighted or sparse data

Data type and tools for working with matrices having precision weights and missing data. This package provides a common representation and tools that can be used with many types of high-throughput data. The meaning of the weights is compatible with usage in the base R function "lm" and the package "limma". Calibrate weights to account for known predictors of precision. Find rows with excess variability. Perform differential testing and find rows with the largest confident differences. Find PCA-like components of variation even with many missing values, rotated so that individual components may be meaningfully interpreted. DelayedArray matrices and BiocParallel are supported.

Last updated 24 days ago

softwaredatarepresentationdimensionreductiongeneexpressiontranscriptomicsrnaseqsinglecellregression

4.70 score 8 scripts 160 downloads