Package: mclink 1.1.1

Liuyang Li

mclink: Metabolic Pathway Completeness and Abundance Calculation

Provides tools for analyzing metabolic pathway completeness, abundance, and transcripts using KEGG Orthology (KO) data from (meta)genomic and (meta)transcriptomic studies. Supports both completeness (presence/absence) and abundance-weighted analyses. Includes built-in KEGG reference datasets. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.

Authors:Liuyang Li [aut, cre]

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mclink.pdf |mclink.html✨
mclink/json (API)

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

Bug tracker:https://github.com/liuyanglee/mclink/issues

Datasets:
  • KO_pathway_ref - KEGG Orthology (KO) Pathway Information Dataset
  • KO_Sample_wide - KEGG Orthology (KO) Abundance/Presence Across Microbial Samples or Genomes

On CRAN:

Conda:

3.48 score 2 stars 391 downloads 27 exports 18 dependencies

Last updated from:4398570c48. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK102
source / vignettesOK149
linux-release-x86_64OK110
macos-release-arm64OK142
macos-oldrel-arm64OK141
windows-develOK76
windows-releaseOK69
windows-oldrelOK86
wasm-releaseOK108

Exports:add_rows_if_not_existsata_calconvert_abundance_to_presencecreate_sub_module_sampleescape_special_charsextract_inner_bracketsgroup_ko_by_moduleKO_pathway_refKO_Sample_widemclinkmerge_module_nameprocess_all_modulesprocess_all_pathwaysprocess_module_bracketsprocess_module_definitionprocess_module_loop_commaprocess_module_loop_plu_commaprocess_module_loop_plusprocess_module_stepprocess_module_structureprocess_step_commaprocess_step_directprocess_step_plusprocess_step_spaceread_and_process_KO_tableread_and_process_pathway_inforremove_outer_brackets

Dependencies:clidata.tabledplyrgenericsgluelifecyclemagrittrpillarpkgconfigR6rlangstringistringrtibbletidyselectutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Add Missing Rows to a Data Frameadd_rows_if_not_exists
Calculate Log2 Ratio of Sample Values to Row Meansata_cal
Convert Abundance Values to Presence/Absence Indicatorsconvert_abundance_to_presence
Create and Export Pathway-Specific Module Sample Filescreate_sub_module_sample
Escape Special Characters in a Stringescape_special_chars
Extract Innermost Parentheses Contentextract_inner_brackets
Group KO Abundance Data by Modulegroup_ko_by_module
KEGG Orthology (KO) Pathway Information DatasetKO_pathway_ref
KEGG Orthology (KO) Abundance/Presence Across Microbial Samples or GenomesKO_Sample_wide
Metabolic Pathway Coverage Analysismclink
Merge Module Information with Module Tablemerge_module_name
Process All Modules in Pathway Informationprocess_all_modules
Process All Pathways Analysisprocess_all_pathways
Process Module Brackets Recursivelyprocess_module_brackets
Process Module Definition Stringprocess_module_definition
Process Module Components with Comma Handlingprocess_module_loop_comma
Process Module Components with Plus and Comma Handlingprocess_module_loop_plu_comma
Process Module Components with Plus Sign Handlingprocess_module_loop_plus
Process Module Steps with Complex KO String Handlingprocess_module_step
Process Module Structure Dataprocess_module_structure
Process Comma-Separated KOs with Specified Scaling Methodprocess_step_comma
Direct KO Processing Without Special Handlingprocess_step_direct
Process Plus-Separated KOs with Specified Scaling Methodprocess_step_plus
Process Space-Separated KOs with Mean Calculationprocess_step_space
Read and Process KO Sample Table with Pathway Informationread_and_process_KO_table
Read and process Pathway information dataframeread_and_process_pathway_infor
Remove Outer Parentheses from Stringremove_outer_brackets