Bundled data | Regression tables | Marker evaluation | Expression data | Reproducibility
Package: clinstats 0.1.2
Feng Gao
clinstats: Clinical Research Statistics Toolkit
Statistical utilities that recur in clinical and translational research workflows: receiver operating characteristic (ROC) summaries, odds ratios, univariable and multivariable Cox and logistic regression tables, time-dependent survival cut points, resampling-based Cox screening, TCGA clinical extraction, and expression-matrix cleaning. Includes curated colorectal cancer clinical datasets assembled from public repositories, a Quarto report template, and tidy data-frame output that is convenient for both interactive and programmatic use.
Authors:
clinstats_0.1.2.tar.gz
clinstats_0.1.2.zip(r-4.7-any)clinstats_0.1.2.zip(r-4.6-any)clinstats_0.1.2.zip(r-4.5-any)
clinstats_0.1.2.tgz(r-4.6-any)clinstats_0.1.2.tgz(r-4.5-any)
clinstats_0.1.2.tar.gz(r-4.7-any)clinstats_0.1.2.tar.gz(r-4.6-any)
clinstats_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
clinstats/json (API)
| # Install 'clinstats' in R: |
| install.packages('clinstats', repos = c('https://gflab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gflab/clinstats/issues
Datasets:
- clin_crc - Curated colorectal cancer clinical data
- clin_crc_cell - Curated colorectal cancer clinical data
- clin_crc_gf - Curated colorectal cancer clinical data
Last updated from:ac4cc66ddb (on main). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 127 | ||
| source / vignettes | OK | 201 | ||
| linux-release | OK | 148 | ||
| macos-release | OK | 176 | ||
| macos-oldrel | OK | 200 | ||
| windows-devel | OK | 83 | ||
| windows-release | OK | 76 | ||
| windows-oldrel | OK | 109 | ||
| wasm-release | OK | 119 |
Exports:clean_expressioncopy_report_templatecox_tableevaluate_modellogistic_tableodds_ratiooncotype_crcresample_coxroc_summarysurvival_cutoffsurvival_responsetcga_clinical
Dependencies:clicodetoolsdigestfuturefuture.applyglobalsgluelatticelifecyclelistenvmagrittrMatrixparallellypillarpkgconfigpROCRcpprlangsurvivaltibbleutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clean an expression matrix and collapse duplicated gene columns | clean_expression |
| Curated colorectal cancer clinical data | clin_crc clin_crc_cell clin_crc_gf |
| Copy the bundled Quarto analysis report template | copy_report_template |
| Regression tables for clinical variables | cox_table logistic_table |
| Evaluate a prediction model on training and test data | evaluate_model |
| Odds ratio for a marker with a binary outcome | odds_ratio |
| Oncotype DX colon cancer recurrence score | oncotype_crc |
| Resampling-based Cox screening of candidate markers | resample_cox |
| Summarise the diagnostic performance of a numeric marker | roc_summary |
| Survival cut point optimising the Youden index | survival_cutoff |
| Build a survival response from a clinical data frame | survival_response |
| Extract clinical variables from a legacy TCGA clinical table | tcga_clinical |