Package: LorMe 2.0.2

LorMe: Lightweight One-Line Resolving Microbial Ecology Program

Provides a robust collection of functions tailored for microbial ecology analysis, encompassing both data analysis and visualization. It introduces an encapsulation feature that streamlines the process into a summary object. With the initial configuration of this summary object, users can execute a wide range of analyses with a single line of code, requiring only two essential parameters for setup. The package delivers comprehensive outputs including analysis objects, statistical outcomes, and visualization-ready data, enhancing the efficiency of research workflows. Designed with user-friendliness in mind, it caters to both novices and seasoned researchers, offering an intuitive interface coupled with adaptable customization options to meet diverse analytical needs.

Authors:Ningqi Wang [aut, cre, cph], Yaozhong Zhang [aut], Gaofei Jiang [aut]

LorMe_2.0.2.tar.gz
LorMe_2.0.2.zip(r-4.7)LorMe_2.0.2.zip(r-4.6)LorMe_2.0.2.zip(r-4.5)
LorMe_2.0.2.tgz(r-4.6-any)LorMe_2.0.2.tgz(r-4.5-any)
LorMe_2.0.2.tar.gz(r-4.7-any)LorMe_2.0.2.tar.gz(r-4.6-any)
LorMe_2.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
LorMe/json (API)

# Install 'LorMe' in R:
install.packages('LorMe', repos = c('https://wangnq111.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wangnq111/lorme/issues

Datasets:

On CRAN:

Conda:

4.71 score 17 stars 15 scripts 405 downloads 48 exports 174 dependencies

Last updated from:b4941397ce. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING351
source / vignettesOK300
linux-release-x86_64WARNING333
macos-release-arm64WARNING203
macos-oldrel-arm64WARNING283
windows-develWARNING215
windows-releaseWARNING221
windows-oldrelWARNING225
wasm-releaseOK224

Exports:.LorMe_optsadd_treeAlpha_diversity_calculatorAlpha_diversity_calculator2anova_reportauto_signif_testcirculation_lmcolor_schemecombine_and_translatecommunity_plotcompare_plotDeseq_analysisDeseq_analysis2differential_barDimension_reductionFilter_functionindicator_analysiskruskal_reportLorMe_defaultsLorMe_optionsLorMe_pipelinemanhattanModule_abundanceModule_compositionncNC_removenetwork_analysisnetwork_analysis2network_statnetwork_visualnetwork_visual_renetwork_withdiffobject_configsafe_runshowstructure_plotsub_tax_summaryt_test_reporttax_summarytbRDA_analysistheme_zgTop_taxaTrans_from_microecoTrans_from_phyloTrans_to_microecoTrans_to_phylovolcano_plotwilcox_test_report

Dependencies:abindagricolaeAlgDesignapeaskpassbackportsbase64encbitbit64bootbroombslibcachemcarcarDatacellrangercheckmateclassclicliprclustercodetoolscoincolorspacecommonmarkcorrplotcowplotcpp11crayoncurldata.tabledeldirDerivDescToolsdigestdoBydplyre1071evaluateExactexpmfarverfastmapfdrtoolfontawesomeforcatsforecastforeignFormulafracdifffsgenericsggalluvialggplot2ggpubrggrepelggsciggsignifgldgluegmpgridExtragtablehavenHHhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrigraphinterpisobandjpegjquerylibjsonliteknitrlabelinglaterlatticelatticeExtralazyevalleapslibcoinlifecyclelme4lmomlmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrmodeltoolsmultcompmultcompViewmvtnormnlmenloptrnnetnumDerivopensslotelpbkrtestpermutepillarpkgconfigplyrpngpolynomprettyunitsprogresspromisesproxypurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreadxlreformulasrematchreshape2rlangrmarkdownRmpfrrootSolverpartrstatixrstudioapiS7sandwichsassscalesshinysourcetoolsSparseMstringistringrsurvivalsysTH.datatibbletidyrtidyselecttimeDatetinytextzdburcautf8vcdvctrsveganviridisLitevroomwithrxfunxtableyamlzoo

Readme and manuals

Help Manual

Help pageTopics
LorMe: Lightweight One-Line Resolving Microbial Ecology ProgramLorMe-package LorMe
Tab completion for LorMe $ access.DollarNames.LorMe
Global options for LorMe pipeline analysis.LorMe_opts
Accessed by 'getOption("LorMe")' or 'LorMe_options()'.onLoad
Access LorMe object elements via $$,LorMe-method
Attach phylogenetic tree to the LorMe objectadd_tree
Calculate alpha diversity based on tax summary objectAlpha_diversity_calculator
Calculate alpha diversity based on tax summary object or dataframe tableAlpha_diversity_calculator2
Print Analysis of Variance reportanova_report
Automatic significance testauto_signif_test
Circulation of fitting Linear Modelscirculation_lm
Get color schemecolor_scheme
Combine data for visualizationcombine_and_translate
Generate Community Composition Plot Based on Tax_summary Objectcommunity_plot
Comparison plot generator This function help generate comparsion plot including bar plot, box plot, and violin plotcompare_plot
Deseq Analysis FunctionDeseq_analysis
Deseq analysisDeseq_analysis2
Generate Differential Bar Plot and Error bar Plotdifferential_bar
Dimension_reduction: PCA, PCOA, and NMDS AnalysisDimension_reduction
Tax summary object with Facet 2x2 GroupsFacet_group
Filter OTU/ASV/metagenomic profile/gene profile by thresholdFilter_function
Indicator Analysisindicator_analysis
Print Kruskal-Wallis Rank Sum Test reportkruskal_report
LorMe package: Lightening One-Code Resolving Microbial Ecology ProgramLorMe
Restore LorMe global options to factory defaultsLorMe_defaults
Change LorMe optionsLorMe_options
One-stop microbial analysis pipeline for LorMe objectsLorMe_pipeline
LorMe S4 classLorMe-class
Manhattan Plot Generatormanhattan
Calculate network module abundance for each sampleModule_abundance
Pie chart for network module compositionModule_composition
Calculate Network Natural Connectivitync
Natural connectivity analysisNC_remove
Conduct Network analysis based on tax summary objectnetwork_analysis
Conduct Network analysisnetwork_analysis2
Igraph network statisticsnetwork_stat
Network Visualizationnetwork_visual
Re-visualize network plot from 'network_visual' or 'network_withdiff'network_visual_re
Network Analysis with Differential Speciesnetwork_withdiff
Set taxonomy summary configurationobject_config
Running function with safe modesafe_run
Show method for LorMe objectsshow,LorMe-method
Visualize microbial community composition structure based on tax summary objectstructure_plot
Subsetting tax summary objectssub_tax_summary
Print Student's t-Test reportt_test_report
Encapsulate meta file, feature tables and taxonomy annotation into tax summary objecttax_summary
tbRDA analysistbRDA_analysis
test otudatatestotu
A classic theme for ggplottheme_zg
Tax summary object with three groupsThree_group
Calculate top taxa and othersTop_taxa
Convert a microeco object to a LorMe objectTrans_from_microeco
Convert phyloseq object to LorMe objectTrans_from_phylo
Convert a LorMe object to a microeco objectTrans_to_microeco
Convert a LorMe object to a phyloseq objectTrans_to_phylo
Tax summary object with two groupsTwo_group
Generate Volcano plot base on Deseq_analysis or indicator_analysis resultsvolcano_plot
Print Wilcoxon Rank Sum and Signed Rank Tests reprotwilcox_test_report