Package: microbial 0.0.22

microbial: Do 16s Data Analysis and Generate Figures

Provides functions to enhance the available statistical analysis procedures in R by providing simple functions to analysis and visualize the 16S rRNA data.Here we present a tutorial with minimum working examples to demonstrate usage and dependencies.

Authors:Kai Guo [aut, cre], Pan Gao [aut]

microbial_0.0.22.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
microbial/json (API)

# Install 'microbial' in R:

install.packages('microbial', repos = c('https://guokai8.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/guokai8/microbial/issues

Datasets:

physeq - The physeq data was modified from the

On CRAN:

software graphandnetwork microbiome microbiome-analysis

5.74 score 15 stars 37 scripts 393 downloads 2 mentions 31 exports 141 dependencies

Last updated from:b587bd20c6. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	395
source / vignettes	OK	312
linux-release-x86_64	ERROR	360
macos-release-arm64	ERROR	225
macos-oldrel-arm64	ERROR	292
windows-devel	ERROR	271
windows-release	ERROR	297
windows-oldrel	ERROR	281
wasm-release	OK	212

Exports:betadiv betatest biomarker buildTree difftest distcolor do_aov do_ttest do_wilcox glmr ldamarker lightcolor normalize otu_table phy_tree plotalpha plotbar plotbeta plotdiff plotLDA plotmarker plotquality prefilter preRef processSeq psmelt richness sample_data subset_samples subset_taxa tax_table

Dependencies:abind ade4 ape backports BH Biobase BiocGenerics BiocParallel biomformat Biostrings boot brio broom callr car carData cli cluster codetools colorspace corrplot cowplot cpp11 crayon data.table DelayedArray Deriv desc DESeq2 diffobj digest doBy dplyr edgeR evaluate farver fastmatch foreach forecast formatR Formula fracdiff fs futile.logger futile.options generics GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable igraph IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle limma lme4 lmtest locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv minqa modelr multtest nlme nloptr nnet numDeriv otel pbkrtest permute phangorn phyloseq pillar pixmap pkgbuild pkgconfig pkgload plyr polynom praise processx ps purrr quadprog quantreg R6 randomForest rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 rlang rprojroot rstatix S4Arrays S4Vectors S7 scales Seqinfo snow sp SparseArray SparseM statmod stringi stringr SummarizedExperiment survival testthat tibble tidyr tidyselect timeDate urca utf8 vctrs vegan viridisLite waldo withr XVector zoo

The microbial package for microbial community analysis

Rendered frommicrobial.Rmdusingknitr::knitr

Last update: 2020-11-29
Started: 2020-10-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
check file format	.checkfile
replace p value with star	.getstar
LEfse function	.lda.fun
calcaute beta diversity	betadiv
PERMANOVA test for phyloseq	betatest
Identify biomarker by using randomForest method	biomarker
contruction of plylogenetic tree (extreme slow)	buildTree
The physeq data was modified from the (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)	data-physeq physeq
The physeq data was modified from the (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)	data-Physeq Physeq
Calculate differential bacteria with DESeq2	difftest
distinguish colors for making figures	distcolor
do anova test and return results as data.frame	do_aov
do t.test	do_ttest
do wilcox test	do_wilcox
Do the generalized linear model regression	glmr
Identify biomarker by using LEfSe method	ldamarker
light colors for making figures	lightcolor
Normalize the phyloseq object with different methods	normalize
extract otu table	otu_table
Retrieve phylogenetic tree (phylo-class) from object.	phy_tree
plot alpha diversity	plotalpha
plot bar for relative abundance for bacteria	plotbar
plot beta diversity	plotbeta
plot differential results	plotdiff
plot LEfSe results from ldamarker function	plotLDA
plot the biomarker from the biomarker function with randomForest	plotmarker
plot the quality for the fastq file	plotquality
filter the phyloseq	prefilter
Download the reference database	preRef
Perform dada2 analysis	processSeq
Melt phyloseq data object into large data.frame	psmelt
calculat the richness for the phyloseq object	richness
extract sample information	sample_data
Subset the phyloseq based on sample	subset_samples
Subset species by taxonomic expression	subset_taxa
extract taxonomy table	tax_table