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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| 1. Introduction to rnaSentry | HTML | R Script |
| 2. Getting started: from two CSVs to a SummarizedExperiment | HTML | R Script |
| 3. Naive analysis vs rnaSentry: what the guardrails prevent | HTML | R Script |
| 4. Case study: breast cancer (GSE20685) | HTML | R Script |
| 5. Case study: confounder audit | HTML | R Script |
| 6. Case study: small cohorts | 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 |
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 (64-bit only) |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/rnaSentry/ |
| Package Short Url | https://bioconductor.org/packages/rnaSentry/ |
| Package Downloads Report | Download Stats |