Package: metaSeq 1.47.0
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_1.47.0.tar.gz
metaSeq_1.47.0.zip(r-4.5)metaSeq_1.47.0.zip(r-4.4)metaSeq_1.47.0.zip(r-4.3)
metaSeq_1.47.0.tgz(r-4.4-any)metaSeq_1.47.0.tgz(r-4.3-any)
metaSeq_1.47.0.tar.gz(r-4.5-noble)metaSeq_1.47.0.tar.gz(r-4.4-noble)
metaSeq_1.47.0.tgz(r-4.4-emscripten)metaSeq_1.47.0.tgz(r-4.3-emscripten)
metaSeq.pdf |metaSeq.html✨
metaSeq/json (API)
| # Install 'metaSeq' in R: |
| install.packages('metaSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- BreastCancer - Multiple RNA-Seq count data designed as Breast Cancer cell lines vs Normal cells
- Result.Meta - Result of meta.oneside.noiseq against Brast Cancer data
- StudyA - Count data of SRP008746
- pvals - P-values or probability calculated by DESeq, edgeR, baySeq, NOISeq, and DEGseq against StudyA
- 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-1.47.0(bioc 3.21)metaSeq-1.46.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
rnaseqdifferentialexpressionsequencingimmunooncology
Last updated 2 months agofrom:dbdffb06d8. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
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 |
