Introduction | RSE: Read-Size Effect | Robustness against RSE | Getting started | Meta-analysis by non-NOISeq method | Setup
Package: metaSeq 1.53.0
Koki Tsuyuzaki
metaSeq: Meta-analysis of RNA-Seq count data in multiple studies
The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method
Authors:
metaSeq_1.53.0.tar.gz
metaSeq_1.53.0.zip(r-4.7)metaSeq_1.53.0.zip(r-4.6)metaSeq_1.53.0.zip(r-4.5)
metaSeq_1.53.0.tgz(r-4.6-any)metaSeq_1.53.0.tgz(r-4.5-any)
metaSeq_1.53.0.tar.gz(r-4.7-any)metaSeq_1.53.0.tar.gz(r-4.6-any)
metaSeq_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
metaSeq/json (API)
| # Install 'metaSeq' in R: |
| install.packages('metaSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- BreastCancer - Multiple RNA-Seq count data designed as Breast Cancer cell lines vs Normal cells
- pvals - P-values or probability calculated by DESeq, edgeR, baySeq, NOISeq, and DEGseq against StudyA
- Result.Meta - Result of meta.oneside.noiseq against Brast Cancer data
- StudyA - Count data of SRP008746
- text.busca_unix - One of C++ re-implimated components in NOISeq
- text.busca_win - One of C++ re-implimated components in NOISeq
- text.n.menor_unix - One of C++ re-implimated components in NOISeq
- text.n.menor_win - One of C++ re-implimated components in NOISeq
On BioConductor:metaSeq-1.53.0(bioc 3.24)metaSeq-1.52.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
rnaseqdifferentialexpressionsequencingimmunooncology
Last updated from:964f74097b. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 158 | ||
| linux-devel-x86_64 | NOTE | 217 | ||
| source / vignettes | OK | 234 | ||
| linux-release-x86_64 | NOTE | 178 | ||
| macos-release-arm64 | NOTE | 131 | ||
| macos-oldrel-arm64 | NOTE | 121 | ||
| windows-devel | NOTE | 99 | ||
| windows-release | NOTE | 100 | ||
| windows-oldrel | NOTE | 97 | ||
| wasm-release | OK | 96 |
Exports:Accelerate.NOISeqFisher.testmeta.oneside.noiseqmeta.readDataother.oneside.pvaluesReset.Accelerate.NOISeqStouffer.test
Dependencies:BiobaseBiocGenericsgenericslatticeMatrixNOISeqRcppsnow
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Meta-analysis of RNA-Seq count data in multiple studies | metaSeq-package metaSeq |
| Accelerating NOISeq | Accelerate.NOISeq |
| Multiple RNA-Seq count data designed as Breast Cancer cell lines vs Normal cells | BreastCancer |
| Fisher's combined probability method | Fisher.test |
| One-sided NOISeq for meta-analysis | meta.oneside.noiseq |
| readData function for meta-analysis | meta.readData |
| Optional function for non-NOISeq method | other.oneside.pvalues |
| P-values or probability calculated by DESeq, edgeR, baySeq, NOISeq, and DEGseq against StudyA | pvals |
| Reset Accelerate.NOISeq function | Reset.Accelerate.NOISeq |
| Result of meta.oneside.noiseq against Brast Cancer data | Result.Meta |
| Stouffer's weighted Z-score method (Inverse normal method) | Stouffer.test |
| Count data of SRP008746 | StudyA |
| One of C++ re-implimated components in NOISeq | text.busca_unix |
| One of C++ re-implimated components in NOISeq | text.busca_win |
| One of C++ re-implimated components in NOISeq | text.n.menor_unix |
| One of C++ re-implimated components in NOISeq | text.n.menor_win |
