Package: file2meco 1.0.0

file2meco: Transform Files to 'microtable' Object with 'microeco' Package

Transform output files of some tools to the 'microtable' object of 'microtable' class in 'microeco' package. The 'microtable' class is the basic class in 'microeco' package and is necessary for the downstream microbial community data analysis.

Authors:Chi Liu [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
file2meco/json (API)

# Install 'file2meco' in R:

install.packages('file2meco', repos = c('https://chiliubio.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/chiliubio/file2meco/issues

Datasets:

CHOCOPhlAn_taxonomy - The CHOCOPhlAn_taxonomy data
MetaCyc_pathway_map - The MetaCyc_pathway_map data
ncyc_map - The ncyc_map data
pcyc_map - The pcyc_map data

On CRAN:

6.16 score 28 stars 144 scripts 1.4k downloads 11 exports 52 dependencies

Last updated from:412f0f61f8. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	195
source / vignettes	OK	225
linux-release-x86_64	NOTE	232
macos-release-arm64	NOTE	120
macos-oldrel-arm64	NOTE	115
windows-devel	NOTE	169
windows-release	NOTE	314
windows-oldrel	NOTE	143
wasm-release	OK	148

Exports:humann2meco meco2phyloseq meco2tse metacyc_pathway_website mpa2meco ncyc2meco phyloseq2meco qiime1meco qiime2meco tse2meco vs2meco

Dependencies:ape biocmake cli cluster cpp11 data.table digest dir.expiry dplyr farver filelock generics ggplot2 glue gtable igraph isoband labeling lattice lifecycle magrittr MASS Matrix mgcv microeco nlme permute pillar pkgconfig plyr purrr R6 RColorBrewer Rcpp reshape2 rhdf5 rhdf5filters Rhdf5lib rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs vegan viridisLite withr yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Replace the names use match table	check_match_table
Read sample table	check_sample_table
The CHOCOPhlAn_taxonomy data	CHOCOPhlAn_taxonomy
Introduction to file2meco package (https://github.com/ChiLiubio/file2meco)	file2meco
Transform 'HUMAnN' metagenomic results to 'microtable' object.	humann2meco
Transform 'microtable' object of 'microeco' package to the 'phyloseq' object of 'phyloseq' package <doi:10.1371/journal.pone.0061217>.	meco2phyloseq
Transform 'microtable' object of 'microeco' package to the 'TreeSummarizedExperiment' object of 'TreeSummarizedExperiment' package <doi:10.12688/f1000research.26669.2>.	meco2tse
Merge multiple microtable objects into one.	merge_microtable
The MetaCyc_pathway_map data	MetaCyc_pathway_map
Get the website for a 'MetaCyc' pathway name	metacyc_pathway_website
Transform metagenomic classification results of 'mpa' format to 'microtable' object.	mpa2meco
The ncyc_map data	ncyc_map
Transform 'NCycDB' or 'PCycDB' metagenomic abundance to 'microtable' object.	ncyc2meco
The pcyc_map data	pcyc_map
Transform the 'phyloseq' object of 'phyloseq' package to 'microtable' object of 'microeco' package.	phyloseq2meco
Transform 'QIIME' results to 'microtable' object.	qiime1meco
Transform 'QIIME2' results to 'microtable' object.	qiime2meco
Transform the 'TreeSummarizedExperiment' object to 'microtable' object of 'microeco' package.	tse2meco
Transform viromescan results to 'microtable' object.	vs2meco