Input data | Example data | Calculating scores for all taxa and samples in an experiment | Calculating scores for a single taxon from a single sample | Simulating IgA-Seq data | Additional examples
Package: IgAScores 0.1.2.9000
IgAScores: Score Taxon-Level IgA Binding in IgA-Seq Experiments
Functions to calculate indices used to score immunoglobulin A (IgA) binding of bacteria in IgA sequencing (IgA-Seq) experiments. This includes the original Kau and Palm indices and more recent methods as described in Jackson et al. (2020) <doi:10.1101/2020.08.19.257501>. Additionally the package contains a function to simulate IgA-Seq data and an example experimental data set for method testing.
Authors:
IgAScores_0.1.2.9000.tar.gz
IgAScores_0.1.2.9000.zip(r-4.7-any)IgAScores_0.1.2.9000.zip(r-4.6-any)IgAScores_0.1.2.9000.zip(r-4.5-any)
IgAScores_0.1.2.9000.tgz(r-4.6-any)IgAScores_0.1.2.9000.tgz(r-4.5-any)
IgAScores_0.1.2.9000.tar.gz(r-4.7-any)IgAScores_0.1.2.9000.tar.gz(r-4.6-any)
IgAScores_0.1.2.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
IgAScores/json (API)
| # Install 'IgAScores' in R: |
| install.packages('IgAScores', repos = c('https://microbialman.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/microbialman/igascores/issues
Datasets:
- oligoMeta - Metadata for the OligoMM12-Colitis experiment used as an example in the IgAScores package
- oligoSpecies - Species level counts for the OligoMM12-Colitis experiment used as an example in the IgAScores package
Last updated from:0e216b8280. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 92 | ||
| source / vignettes | OK | 147 | ||
| linux-release | OK | 99 | ||
| macos-release | OK | 144 | ||
| macos-oldrel | OK | 186 | ||
| windows-devel | OK | 49 | ||
| windows-release | OK | 46 | ||
| windows-oldrel | OK | 63 | ||
| wasm-release | OK | 66 |
Exports:igaprobabilityigaprobabilityratioigascoreskauindexpalmindexrelabundsimulateigaseqtaxnamesplit
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| IgA Probability | igaprobability |
| IgA Probability Ratio | igaprobabilityratio |
| Generate various scores for IgA binding in IgA-Seq experiments | igascores |
| Kau Index | kauindex |
| Metadata for the OligoMM12-Colitis experiment used as an example in the IgAScores package | oligoMeta |
| Species level counts for the OligoMM12-Colitis experiment used as an example in the IgAScores package | oligoSpecies |
| Palm Index | palmindex |
| Relative Abundance from Counts | relabund |
| Simulate an IgA-Seq dataset from a pre-defined set of IgA-binding probabilities | simulateigaseq |
| Extract name at a given taxonomic level from a full name in the "p__;c__;o__;f__;g__;s__" format | taxnamesplit |