Package: SACAT 0.99.2

Yiqian Zhang
SACAT: Structural-Absence and Conditional-Abundance Testing
Provides depth-aware taxon-level inference for microbiome count data. SACAT separates group differences in structural-absence probability from differences in mean log relative abundance among samples in which a taxon is present. It accounts for finite-depth nondetection, centers abundance effects against a target-excluded cross-taxon reference, reports component-specific and omnibus tests, and visualizes statistical evidence, observed detection, estimated zero sources, and abundance distributions.
Authors:
SACAT_0.99.2.tar.gz
SACAT_0.99.2.zip(r-4.7-x86_64)SACAT_0.99.2.zip(r-4.7-arm64)SACAT_0.99.2.zip(r-4.6-x86_64)SACAT_0.99.2.zip(r-4.6-arm64)SACAT_0.99.2.zip(r-4.5-x86_64)
SACAT_0.99.2.tgz(r-4.6-x86_64)SACAT_0.99.2.tgz(r-4.6-arm64)SACAT_0.99.2.tgz(r-4.5-x86_64)SACAT_0.99.2.tgz(r-4.5-arm64)
SACAT_0.99.2.tar.gz(r-4.7-arm64)SACAT_0.99.2.tar.gz(r-4.7-x86_64)SACAT_0.99.2.tar.gz(r-4.6-arm64)SACAT_0.99.2.tar.gz(r-4.6-x86_64)
SACAT_0.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SACAT/json (API)
| # Install 'SACAT' in R: |
| install.packages('SACAT', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/statwright/sacat/issues
- gems_microbiome - Gut microbiome profiles from children in the GEMS study
microbiomemetagenomicsdifferentialexpressionregressionstatisticalmethodvisualizationcpp
Last updated from:976eedb31c. Checks:1 NOTE, 15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 177 | ||
| linux-devel-arm64 | OK | 1347 | ||
| linux-devel-x86_64 | OK | 850 | ||
| source / vignettes | OK | 657 | ||
| linux-release-arm64 | OK | 1362 | ||
| linux-release-x86_64 | OK | 816 | ||
| macos-release-arm64 | OK | 859 | ||
| macos-release-x86_64 | OK | 2052 | ||
| macos-oldrel-arm64 | OK | 968 | ||
| macos-oldrel-x86_64 | OK | 1660 | ||
| windows-devel-arm64 | OK | 1059 | ||
| windows-devel-x86_64 | OK | 3506 | ||
| windows-release-arm64 | OK | 1075 | ||
| windows-release-x86_64 | OK | 3484 | ||
| windows-oldrel-x86_64 | OK | 3558 | ||
| wasm-release | OK | 99 |
Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSeqinfoSparseArraystatmodSummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gut microbiome profiles from children in the GEMS study | gems_microbiome |
| Plot a SACAT association profile | plot.sacat |
| Structural-Absence and Conditional-Abundance Testing | sacat |
| Run SACAT on a SummarizedExperiment | sacat_se |
