Example | Installation | Load the package | Import and inspect data | Format sample_data | Process data using process_ngs() | PCA visualisation with mva() | Permutational analysis of variance with permanova() | Adjusting for multiple comparisons with adjust_pval() | Adding feature labels with add_feat_name() or add_taxa() | Visualise results with ready_plots() | Bonus (microbiome): dana() for alpha diversity | Bonus (microbiome): dana() for higher taxonomic ranks
Package: readyomics 0.2.1
readyomics: Ready-to-Use Omics Formatting, Analysis, and Visualization Pipeline
Provides a flexible and streamlined pipeline for formatting, analyzing, and visualizing omics data, regardless of omics type (e.g. transcriptomics, proteomics, metabolomics). The package includes tools for shaping input data into analysis-ready structures, fitting linear or mixed-effect models, extracting key contrasts, and generating a rich variety of ready-to-use publication-quality plots. Designed for transparency and reproducibility across a wide range of study designs, with customizable components for statistical modeling.
Authors:
readyomics_0.2.1.tar.gz
readyomics_0.2.1.zip(r-4.7)readyomics_0.2.1.zip(r-4.6)readyomics_0.2.1.zip(r-4.5)
readyomics_0.2.1.tgz(r-4.6-any)readyomics_0.2.1.tgz(r-4.5-any)
readyomics_0.2.1.tar.gz(r-4.7-any)readyomics_0.2.1.tar.gz(r-4.6-any)
readyomics_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
readyomics/json (API)
| # Install 'readyomics' in R: |
| install.packages('readyomics', repos = c('https://lmartinezgili.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lmartinezgili/readyomics/issues
Pkgdown/docs site:https://lmartinezgili.github.io
Last updated from:7b0d000af2. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 212 | ||
| source / vignettes | OK | 261 | ||
| linux-release-x86_64 | OK | 208 | ||
| macos-release-arm64 | OK | 132 | ||
| macos-oldrel-arm64 | OK | 150 | ||
| windows-devel | OK | 114 | ||
| windows-release | OK | 145 | ||
| windows-oldrel | OK | 114 | ||
| wasm-release | OK | 173 |
Exports:add_feat_nameadd_taxaadjust_pvalbuild_phyloseqdanamvapermanovaprocess_msprocess_ngsready_plots
Dependencies:bootcliclustercodetoolscpp11digestdplyrfarverfuturefuture.applygenericsggplot2globalsgluegtableisobandlabelinglatticelifecyclelistenvlme4lmerTestmagrittrMASSMatrixmgcvminqaNADAnlmenloptrnumDerivparallellypermutepillarpkgconfigpurrrR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangS7scalesstringistringrsurvivaltibbletidyrtidyselecttruncnormutf8vctrsveganviridisLitewithrzCompositions
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Append feature names to a 'dana' object | add_feat_name |
| Add taxonomic information to 'dana' object | add_taxa |
| Adjust P-values in a 'dana' object | adjust_pval |
| Build phyloseq objects for all taxonomy ranks | build_phyloseq |
| Differential analysis (dana) | dana |
| Multivariate analysis (PCA, PLS, OPLS) | mva |
| PERMANOVA with flexible permutation control | permanova |
| Process MS-like omics data | process_ms |
| Process next generation sequencing data | process_ngs |
| Generate plots from a differential analysis ('dana') object | ready_plots |
