Package: MetaLonDA 1.1.8

Ahmed A. Metwally

MetaLonDA: Metagenomics Longitudinal Differential Abundance Method

Identify time intervals of differentially abundant metagenomic features in longitudinal studies (Metwally AA, et al., Microbiome, 2018 <doi:10.1186/s40168-018-0402-y>).

Authors:Ahmed A. Metwally, Yang Dai, Patricia W. Finn, David L. Perkins

MetaLonDA_1.1.8.tar.gz
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MetaLonDA_1.1.8.tgz(r-4.4-any)MetaLonDA_1.1.8.tgz(r-4.3-any)
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MetaLonDA.pdf |MetaLonDA.html✨
MetaLonDA/json (API)

# Install 'MetaLonDA' in R:

install.packages('MetaLonDA', repos = c('https://aametwally.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aametwally/metalonda/issues

Datasets:

metalonda_test_data - Simulated data of OTU abundance for 2 phenotypes each has 5 subjects at 10 time-points

On CRAN:

differential-abundance-methods longitudinal-studies metagenomics microbiome negative-binomial-distribution smoothing-splines

5.75 score 16 stars 9 scripts 201 downloads 7 mentions 14 exports 88 dependencies

Last updated 5 years agofrom:263e1d33c4. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 13 2024
R-4.5-win	NOTE	Oct 14 2024
R-4.5-linux	NOTE	Nov 13 2024
R-4.4-win	NOTE	Oct 14 2024
R-4.4-mac	NOTE	Oct 14 2024
R-4.3-win	NOTE	Nov 13 2024
R-4.3-mac	NOTE	Nov 13 2024

Exports:areaPermutation curveFitting findSigInterval intervalArea metalonda metalondaAll normalize permutation visualizeArea visualizeARHistogram visualizeFeature visualizeFeatureSpline visualizeTimeIntervals visualizeVolcanoPlot

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel bitops caTools cli codetools colorspace cpp11 crayon curl DelayedArray DESeq2 doParallel edgeR fansi farver foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glmnet glue gplots gss gtable gtools httr IRanges isoband iterators jsonlite KernSmooth labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats metagenomeSeq mgcv mime munsell nlme openssl pillar pkgconfig plyr pracma R6 RColorBrewer Rcpp RcppArmadillo RcppEigen rlang S4Arrays S4Vectors scales shape snow SparseArray statmod SummarizedExperiment survival sys tibble UCSC.utils utf8 vctrs viridisLite withr Wrench XVector zlibbioc zoo

An Introduction to the MetaLonDA Package

Ahmed A. Metwally

Rendered fromMetaLonDA.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2019-04-13
Started: 2018-01-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate Area Ratio (AR) of each feature's time interval for all permutations	areaPermutation
Fit longitudinal data	curveFitting
Find significant time intervals	findSigInterval
Calculate Area Ratio (AR) of each feature's time interval	intervalArea
Metagenomic Longitudinal Differential Abundance Analysis for one feature	metalonda
Simulated data of OTU abundance for 2 phenotypes each has 5 subjects at 10 time-points	metalonda_test_data
Metagenomic Longitudinal Differential Abundance Analysis for all Features	metalondaAll
Normalize count matrix	normalize
Permute group labels	permutation
Visualize significant time interval	visualizeArea
Visualize Area Ratio (AR) empirical distribution	visualizeARHistogram
Visualize Longitudinal Feature	visualizeFeature
Visualize the feature trajectory with the fitted Splines	visualizeFeatureSpline
Visualize all significant time intervals for all tested features	visualizeTimeIntervals
Visualize log2 fold-change and significance of each interval as volcano plot	visualizeVolcanoPlot