Package: LorMe 1.0.1

LorMe: Lightening One-Code Resolving Microbial Ecology Solution

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_1.0.1.tar.gz
LorMe_1.0.1.zip(r-4.5)LorMe_1.0.1.zip(r-4.4)LorMe_1.0.1.zip(r-4.3)
LorMe_1.0.1.tgz(r-4.4-any)LorMe_1.0.1.tgz(r-4.3-any)
LorMe_1.0.1.tar.gz(r-4.5-noble)LorMe_1.0.1.tar.gz(r-4.4-noble)
LorMe_1.0.1.tgz(r-4.4-emscripten)LorMe_1.0.1.tgz(r-4.3-emscripten)
LorMe.pdf |LorMe.html✨
LorMe/json (API)

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

Peer review:

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

Datasets:

On CRAN:

4.38 score 8 stars 1 scripts 334 downloads 37 exports 168 dependencies

Last updated 11 days agofrom:ba20c3c6fc. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxOKNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:Alpha_diversity_calculatorAlpha_diversity_calculator2anova_reportauto_signif_testcirculation_lmcolor_schemecombine_and_translatecommunity_plotcompare_plotDeseq_analysisDeseq_analysis2differential_barDimension_reductionFilter_functionindicator_analysiskruskal_reportmanhattanModule_abundanceModule_compositionncNC_removenetwork_analysisnetwork_analysis2network_statnetwork_visualnetwork_visual_renetwork_withdiffobject_configstructure_plotsub_tax_summaryt_test_reporttax_summarytbRDA_analysistheme_zgTop_taxavolcano_plotwilcox_test_report

Dependencies:abindagricolaeAlgDesignapeaskpassbackportsbase64encbitbit64bootbroombslibcachemcarcarDatacellrangercheckmateclassclicliprclustercodetoolscoincolorspacecommonmarkcorrplotcowplotcpp11crayoncurldata.tabledeldirDerivDescToolsdigestdoBydplyre1071evaluateExactexpmfansifarverfastmapfdrtoolfontawesomeforcatsforeignFormulafsgenericsggalluvialggplot2ggpubrggrepelggsciggsignifgldgluegmpgridExtragtablehavenHHhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrigraphinterpisobandjpegjquerylibjsonliteknitrlabelinglaterlatticelatticeExtralazyevalleapslibcoinlifecyclelme4lmomlmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmodeltoolsmultcompmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpermutepillarpkgconfigplyrpngpolynomprettyunitsprogresspromisesproxypurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreadrreadxlrematchreshape2rlangrmarkdownRmpfrrootSolverpartrstatixrstudioapisandwichsassscalesshinysourcetoolsSparseMstringistringrsurvivalsysTH.datatibbletidyrtidyselecttinytextzdbutf8vcdvctrsveganviridisviridisLitevroomwithrxfunxtableyamlzoo

Readme and manuals

Help Manual

Help pageTopics
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
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
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
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