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
microbial_0.0.22.zip(r-4.5)microbial_0.0.22.zip(r-4.4)microbial_0.0.22.zip(r-4.3)
microbial_0.0.22.tgz(r-4.4-any)microbial_0.0.22.tgz(r-4.3-any)
microbial_0.0.22.tar.gz(r-4.5-noble)microbial_0.0.22.tar.gz(r-4.4-noble)
microbial_0.0.22.tgz(r-4.4-emscripten)microbial_0.0.22.tgz(r-4.3-emscripten)
microbial.pdf |microbial.html✨
microbial/json (API)

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

Peer review:

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

Datasets:
  • physeq - The physeq data was modified from the

On CRAN:

softwaregraphandnetworkmicrobiomemicrobiome-analysis

5.68 score 12 stars 20 scripts 368 downloads 2 mentions 31 exports 145 dependencies

Last updated 1 months agofrom:b587bd20c6. Checks:OK: 1 ERROR: 1 WARNING: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-winWARNINGNov 08 2024
R-4.5-linuxERRORNov 08 2024
R-4.4-winWARNINGNov 08 2024
R-4.4-macWARNINGNov 08 2024
R-4.3-winWARNINGNov 08 2024
R-4.3-macWARNINGNov 08 2024

Exports:betadivbetatestbiomarkerbuildTreedifftestdistcolordo_aovdo_ttestdo_wilcoxglmrldamarkerlightcolornormalizeotu_tablephy_treeplotalphaplotbarplotbetaplotdiffplotLDAplotmarkerplotqualityprefilterpreRefprocessSeqpsmeltrichnesssample_datasubset_samplessubset_taxatax_table

Dependencies:abindade4apeaskpassbackportsBHBiobaseBiocGenericsBiocParallelbiomformatBiostringsbootbriobroomcallrcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDelayedArrayDerivdescDESeq2diffobjdigestdoBydplyredgeRevaluatefansifarverfastmatchforeachformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmulttestmunsellnlmenloptrnnetnumDerivopensslpbkrtestpermutephangornphyloseqpillarpixmappkgbuildpkgconfigpkgloadplyrpolynompraiseprocessxpspurrrquadprogquantregR6randomForestRColorBrewerRcppRcppArmadilloRcppEigenreshape2rhdf5rhdf5filtersRhdf5librlangrprojrootrstatixS4ArraysS4VectorsscalessnowspSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystestthattibbletidyrtidyselectUCSC.utilsutf8vctrsveganviridisLitewaldowithrXVectorzlibbioc

The microbial package for microbial community analysis

Kai Guo, University of Michigan, Pan Gao, University of North Dakota

Rendered frommicrobial.Rmdusingknitr::knitron Nov 08 2024.

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

Readme and manuals

Help Manual

Help pageTopics
check file format.checkfile
replace p value with star.getstar
LEfse function.lda.fun
calcaute beta diversitybetadiv
PERMANOVA test for phyloseqbetatest
Identify biomarker by using randomForest methodbiomarker
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 DESeq2difftest
distinguish colors for making figuresdistcolor
do anova test and return results as data.framedo_aov
do t.testdo_ttest
do wilcox testdo_wilcox
Do the generalized linear model regressionglmr
Identify biomarker by using LEfSe methodldamarker
light colors for making figureslightcolor
Normalize the phyloseq object with different methodsnormalize
extract otu tableotu_table
Retrieve phylogenetic tree (phylo-class) from object.phy_tree
plot alpha diversityplotalpha
plot bar for relative abundance for bacteriaplotbar
plot beta diversityplotbeta
plot differential resultsplotdiff
plot LEfSe results from ldamarker functionplotLDA
plot the biomarker from the biomarker function with randomForestplotmarker
plot the quality for the fastq fileplotquality
filter the phyloseqprefilter
Download the reference databasepreRef
Perform dada2 analysisprocessSeq
Melt phyloseq data object into large data.framepsmelt
calculat the richness for the phyloseq objectrichness
extract sample informationsample_data
Subset the phyloseq based on samplesubset_samples
Subset species by taxonomic expressionsubset_taxa
extract taxonomy tabletax_table