rnaSentry
This is the development version of rnaSentry; to use it, please install the devel version of Bioconductor.
Guarded and Auditable Discovery of Prognostic RNA-Seq Signatures
Bioconductor version: Development (3.24)
Orchestrates the statistical pipeline underlying prognostic biomarker discovery from bulk RNA-seq SummarizedExperiment objects: sample-identity and quality-control auditing, confounder and design-formula detection prior to differential expression, signature construction with explicit cross-validation stability reporting, survival modeling (Kaplan-Meier, log-rank, Cox proportional hazards), and external validation against public cohorts. Every automated statistical decision is reported with its supporting statistic and a plain-language rationale, and validation stages are gated rather than silently degraded when guardrail criteria are not met. The package records all guardrail decisions, flag ledgers, and validation results in a structured audit trail that can be rendered into a standalone HTML report.
Author: Abdelkarim Hani Ghrieb [aut, cre]
Maintainer: Abdelkarim Hani Ghrieb <ghriebabdelkarimhani at gmail.com>
citation("rnaSentry")):Abdelkarim Hani Ghrieb. rnaSentry: Guarded and Auditable Discovery of Prognostic RNA-Seq Signatures. doi:10.18129/B9.bioc.rnaSentry, R package version 0.99.19, https://bioconductor.org/packages/rnaSentry.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("rnaSentry")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rnaSentry")| 4. Case study: breast cancer (GSE20685) | HTML | R Script |
| 5. Case study: confounder audit | HTML | R Script |
| 3. Naive analysis vs rnaSentry: what the guardrails prevent | HTML | R Script |
| 6. Case study: small cohorts | HTML | R Script |
| 2. Getting started: from two CSVs to a SummarizedExperiment | HTML | R Script |
| 1. Introduction to rnaSentry | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BatchEffect, DifferentialExpression, GeneExpression, Normalization, QualityControl, RNASeq, Software, Survival |
| Version | 0.99.19 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | S4Vectors, SummarizedExperiment, survival, withr, methods |
| System Requirements | |
| URL | https://ghrieb.github.io/rnaSentry/ https://github.com/Ghrieb/rnaSentry |
| Bug Reports | https://github.com/Ghrieb/rnaSentry/issues |
See More
| Suggests | Biobase, BiocParallel, BiocStyle, GEOquery, ggplot2, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | rnaSentry_0.99.19.tar.gz |
| Windows Binary (x86_64) | rnaSentry_0.99.19.zip |
| macOS Binary (big-sur-x86_64) | rnaSentry_0.99.19.tgz |
| macOS Binary (sonoma-arm64) | rnaSentry_0.99.19.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rnaSentry |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rnaSentry |
| Package Short Url | https://bioconductor.org/packages/rnaSentry/ |
| Package Downloads Report | Download Stats |