Package: microeco 2.4.1

microeco: Microbial Community Ecology Data Analysis

A series of data analysis approaches for microbiome data based on the R6 class. The classes are designed for data preprocessing, niche analysis, taxonomic abundance plot, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis, functional redundancy analysis, metabolites analysis, etc.

Authors:Chi Liu [aut, cre], Felipe R. P. Mansoldo [ctb], Minjie Yao [ctb], Xiangzhen Li [ctb]

microeco_2.4.1.tar.gz
microeco_2.4.1.zip(r-4.7-any)microeco_2.4.1.zip(r-4.6-any)microeco_2.4.1.zip(r-4.5-any)
microeco_2.4.1.tgz(r-4.6-any)microeco_2.4.1.tgz(r-4.5-any)
microeco_2.4.1.tar.gz(r-4.7-any)microeco_2.4.1.tar.gz(r-4.6-any)
microeco_2.4.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
microeco/json (API)

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

Bug tracker:https://github.com/chiliubio/microeco/issues

Datasets:
  • dataset - The dataset structured with microtable class for the demonstration of examples
  • env_data_16S - The environmental factors for the 16S example data
  • fungi_func_FungalTraits - The FungalTraits database for fungi trait prediction
  • fungi_func_FUNGuild - The FUNGuild database for fungi trait prediction
  • otu_table_16S - The OTU table of the 16S example data
  • otu_table_ITS - The OTU table of the ITS example data
  • phylo_tree_16S - The phylogenetic tree of 16S example data
  • prok_func_FAPROTAX - Customized FAPROTAX trait database
  • prok_func_NJC19_list - The NJC19 database
  • sample_info_16S - The sample information of 16S example data
  • sample_info_ITS - The sample information of ITS example data
  • soil_metab - Microtable object of non-targeted metabolome data from bulk soil and maize rhizosphere soil in an agricultural field experiment with crop rotation and fertilization treatments (DOI: 10.1007/s11104-024-06847-9).
  • soil_microb - Microtable object of prokaryotic sequencing data from soil and maize in an agricultural field experiment with crop rotation and fertilization treatments (DOI: 10.1007/s11104-024-06847-9).
  • Tax4Fun2_KEGG - The KEGG data files used in the trans_func class
  • taxonomy_table_16S - The taxonomic information of 16S example data
  • taxonomy_table_ITS - The taxonomic information of ITS example data

On CRAN:

Conda:

10.29 score 293 stars 3 packages 430 scripts 2.7k downloads 1 mentions 21 exports 42 dependencies

Last updated from:63565a1c88. Checks:1 OK, 5 NOTE. Indexed: yes.

TargetResultTimeFilesSyslog
source / vignettesOK297
linux-releaseNOTE218
macos-oldrelNOTE176
windows-develNOTE181
windows-releaseNOTE155
windows-oldrelNOTE168

Exports:clonedropallfactorsmicrotabletidy_taxonomytrans_abundtrans_alphatrans_betatrans_classifiertrans_difftrans_envtrans_functrans_metabtrans_msttrans_multiomicstrans_networktrans_nichetrans_normtrans_nullmodeltrans_phylotrans_rarefytrans_venn

Dependencies:apecliclustercpp11data.tabledigestdplyrfarvergenericsggplot2gluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvnlmepermutepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangS7scalesstringistringrtibbletidyselectutf8vctrsveganviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Copy an R6 class objectclone
The dataset structured with microtable class for the demonstration of examplesdataset
Remove all factors in a data framedropallfactors
The environmental factors for the 16S example dataenv_data_16S
The FungalTraits database for fungi trait predictionfungi_func_FungalTraits
The FUNGuild database for fungi trait predictionfungi_func_FUNGuild
Introduction to microeco package (https://github.com/ChiLiubio/microeco)microeco
Create 'microtable' object to store and manage all the basic data.microtable
The OTU table of the 16S example dataotu_table_16S
The OTU table of the ITS example dataotu_table_ITS
The phylogenetic tree of 16S example dataphylo_tree_16S
Customized FAPROTAX trait databaseprok_func_FAPROTAX
The NJC19 databaseprok_func_NJC19_list
The sample information of 16S example datasample_info_16S
The sample information of ITS example datasample_info_ITS
Microtable object of non-targeted metabolome data from bulk soil and maize rhizosphere soil in an agricultural field experiment with crop rotation and fertilization treatments (DOI: 10.1007/s11104-024-06847-9).soil_metab
Microtable object of prokaryotic sequencing data from soil and maize in an agricultural field experiment with crop rotation and fertilization treatments (DOI: 10.1007/s11104-024-06847-9).soil_microb
The KEGG data files used in the trans_func classTax4Fun2_KEGG
The taxonomic information of 16S example datataxonomy_table_16S
The taxonomic information of ITS example datataxonomy_table_ITS
Clean up the taxonomic table to make taxonomic assignments consistent.tidy_taxonomy
Create 'trans_abund' object for taxonomic abundance visualization.trans_abund
Create 'trans_alpha' object for alpha diversity statistics and visualization.trans_alpha
Create 'trans_beta' object for beta-diversity analysistrans_beta
Create 'trans_classifier' object for machine-learning-based model prediction.trans_classifier
Create 'trans_diff' object for the differential analysis on the taxonomic abundancetrans_diff
Create 'trans_env' object to analyze the association between environmental factor and microbial community.trans_env
Create 'trans_func' object for functional prediction.trans_func
Create 'trans_metab' object for metabolite analysis.trans_metab
Create 'trans_mst' object for microbial source tracking (MST) analysis.trans_mst
Multi-omics data integration analysis.trans_multiomics
Create 'trans_network' object for network analysis.trans_network
Create 'trans_niche' object for niche breadth and niche overlap analysis.trans_niche
Feature abundance normalization/transformation.trans_norm
Create 'trans_nullmodel' object for null model related analysis.trans_nullmodel
trans_phylo classtrans_phylo
Rarefaction and plotting.trans_rarefy
Create 'trans_venn' object for the Venn diagram, petal plot and UpSet plot.trans_venn