Package: topconfects 1.23.2
Paul Harrison
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.
Authors:
topconfects_1.23.2.tar.gz
topconfects_1.23.2.zip(r-4.5)topconfects_1.23.2.zip(r-4.4)topconfects_1.23.2.zip(r-4.3)
topconfects_1.23.2.tgz(r-4.5-any)topconfects_1.23.2.tgz(r-4.4-any)topconfects_1.23.2.tgz(r-4.3-any)
topconfects_1.23.2.tar.gz(r-4.5-noble)topconfects_1.23.2.tar.gz(r-4.4-noble)
topconfects_1.23.2.tgz(r-4.4-emscripten)topconfects_1.23.2.tgz(r-4.3-emscripten)
topconfects.pdf |topconfects.html✨
topconfects/json (API)
NEWS
| # Install 'topconfects' in R: |
| install.packages('topconfects', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pfh/topconfects/issues
On BioConductor:topconfects-1.23.2(bioc 3.21)topconfects-1.22.0(bioc 3.20)
geneexpressiondifferentialexpressiontranscriptomicsrnaseqmrnamicroarrayregressionmultiplecomparison
Last updated 3 months agofrom:ef5968f093. Checks:9 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 11 2025 |
| R-4.5-win | OK | Mar 11 2025 |
| R-4.5-mac | OK | Mar 11 2025 |
| R-4.5-linux | OK | Mar 11 2025 |
| R-4.4-win | OK | Mar 11 2025 |
| R-4.4-mac | OK | Mar 11 2025 |
| R-4.4-linux | OK | Mar 11 2025 |
| R-4.3-win | OK | Mar 11 2025 |
| R-4.3-mac | OK | Mar 11 2025 |
Exports:confects_plotconfects_plot_meconfects_plot_me2deseq2_confectsedger_confectslimma_confectsnest_confectsnormal_confectsrank_rank_plot
Dependencies:assertthatclicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Top confident effect sizes plot | confects_plot |
| Mean-expression vs effect size plot (deprecated) | confects_plot_me |
| Mean-expression vs effect size plot (version 2) | confects_plot_me2 |
| Confident log2 fold changes based on a DESeq2 analysis | deseq2_confects |
| Confident log2 fold change based on the edgeR Quasi-Likelihood method | edger_confects |
| Confident log2 fold changes based on a limma fit object | limma_confects |
| General purpose function to find confident effect sizes, controlling FDR | nest_confects |
| Confident effect sizes from from normal or t distributions | normal_confects |
| A plot to compare two rankings | rank_rank_plot |
