Introduction | Installation | Functions Overview | Demonstration datasets | MetadataABA | TranscriptomeABA | SRGA (Stress Responsive Gene Atlas) | Example Workflow | 1. Comparison Pairs | 2. Calculation of the SRratio | 3. Calculate SRscore | Simple Plotting | SRscore distribution | Ranked SRscore | Top SRscore | All-in-One Execution | Metadata viewer | Downstream analysis | Enrichment Analysis | Heatmap | Template Matching | Summary | Session info | References
Package: SRscore 0.1.2
SRscore: Simple Transcriptome Meta-Analysis for Identifying Stress-Responsive Genes
Stress Response score (SRscore) is a stress responsiveness measure for transcriptome datasets and is based on the vote-counting method. The SRscore is determined to evaluate and score genes on the basis of the consistency of the direction of their regulation (Up-regulation, Down-regulation, or No change) under stress conditions across multiple analyzed research projects. This package is based on the HN-score (score based on the ratio of gene expression between hypoxic and normoxic conditions) proposed by Tamura and Bono (2022) <doi:10.3390/life12071079>, and can calculate both the original method and an extended calculation method described in Fukuda et al. (2025) <doi:10.1093/plphys/kiaf105>.
Authors:
SRscore_0.1.2.tar.gz
SRscore_0.1.2.zip(r-4.7-any)SRscore_0.1.2.zip(r-4.6-any)SRscore_0.1.2.zip(r-4.5-any)
SRscore_0.1.2.tgz(r-4.6-any)SRscore_0.1.2.tgz(r-4.5-any)
SRscore_0.1.2.tar.gz(r-4.7-any)SRscore_0.1.2.tar.gz(r-4.6-any)
SRscore_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SRscore/json (API)
| # Install 'SRscore' in R: |
| install.packages('SRscore', repos = c('https://fusk-kpu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fusk-kpu/srscore/issues
Datasets:
- HNscore - Reproducing HN-scores from HN-ratios Using the SRscore Package
- logHNratioHypoxia - Reproducing HN-scores from HN-ratios Using the SRscore Package
- MetadataABA - Metadata of abscisic acid stress microarray dataset in _Arabidopsis thaliana_
- MetadataHypoxia - Metadata of Hypoxia stress RNA-Seq dataset in _Arabidopsis thaliana_
- sample_pair_test - Test data to create data frames from all combinations between two specified variables within each group using sample data
- SRGA - Test data for the SRscore package
- SRratio_test - Test data for calculating SRratio using sample data
- SRscore_test - Test data for calculating SRscore using sample data
- TPMHypoxia - Hypoxia stress RNA-Seq data in _Arabidopsis thaliana_
- TranscriptomeABA - Abscisic acid stress microarray dataset in _Arabidopsis thaliana_
Last updated from:c47cbea2c1. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 213 | ||
| source / vignettes | OK | 281 | ||
| linux-release | OK | 199 | ||
| macos-release | OK | 189 | ||
| macos-oldrel | OK | 196 | ||
| windows-devel | OK | 96 | ||
| windows-release | OK | 101 | ||
| windows-oldrel | OK | 111 | ||
| wasm-release | OK | 145 |
Exports:calcSRratiocalcSRscoredirectly_calcSRscoreexpand_by_groupfind_diffexpplot_SRscore_distrplot_SRscore_rankplot_SRscore_top
Dependencies:clicpp11dplyrgenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithr
