Abstract | Introduction | Installation | Running Wrench | Usage with differential abundance pipelines | Some caveats / work in development | The "detrend" option | Session Info
Package: Wrench 1.30.0
Hector Corrada Bravo
Wrench: Wrench normalization for sparse count data
Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.
Authors:
Wrench_1.30.0.tar.gz
Wrench_1.30.0.zip(r-4.7-any)Wrench_1.30.0.zip(r-4.6-any)Wrench_1.30.0.zip(r-4.5-any)
Wrench_1.30.0.tgz(r-4.6-any)Wrench_1.30.0.tgz(r-4.5-any)
Wrench_1.30.0.tar.gz(r-4.7-any)Wrench_1.30.0.tar.gz(r-4.6-any)
Wrench_1.30.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
Wrench/json (API)
| # Install 'Wrench' in R: |
| install.packages('Wrench', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hcbravolab/wrench/issues
On BioConductor:Wrench-1.31.0(bioc 3.24)Wrench-1.30.0(bioc 3.23)
normalizationsequencingsoftware
Last updated from:eee47afb9f (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 136 | ||
| linux-devel | OK | 272 | ||
| source / vignettes | OK | 186 | ||
| linux-release | OK | 227 | ||
| macos-release | OK | 97 | ||
| macos-oldrel | OK | 108 | ||
| windows-devel | OK | 178 | ||
| windows-release | OK | 174 | ||
| windows-oldrel | OK | 130 | ||
| wasm-release | OK | 135 |
Exports:wrench
Dependencies:latticelimmalocfitmatrixStatsstatmod
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Obtain robust means. . | .estimSummary |
| Log Postive-conditional weight computations for wrench estimators. | .getCondLogWeights |
| Postive-conditional weight computations for wrench estimators. | .getCondWeights |
| Obtains logistic fits for presence/absence and fitted probabilities of a zero occurring. | .getHurdle |
| Marginal weight computations for wrench estimators. | .getMargWeights |
| This function generates the reference. | .getReference |
| Obtain variances of logged counts. | .gets2 |
| Get weighted means for matrix | .getWeightedMean |
| Get weighted median for matrix | .getWeightedMedian |
| Normalization for sparse, under-sampled count data. | wrench |