Package: LipidomicsR 0.3.6

Hengyu Zhu

LipidomicsR: Elegant Tools for Processing and Visualization of Lipidomics Data

An elegant tool for processing and visualizing lipidomics data generated by mass spectrometry. 'LipidomicsR' simplifies channel and replicate handling while providing thorough lipid species annotation. Its visualization capabilities encompass principal components analysis plots, heatmaps, volcano plots, and radar plots, enabling concise data summarization and quality assessment. Additionally, it can generate bar plots and line plots to visualize the abundance of each lipid species.

Authors:Mingshi Li [aut, com], Hengyu Zhu [aut, cre]

LipidomicsR_0.3.6.tar.gz
LipidomicsR_0.3.6.zip(r-4.7)LipidomicsR_0.3.6.zip(r-4.6)LipidomicsR_0.3.6.zip(r-4.5)
LipidomicsR_0.3.6.tgz(r-4.6-any)LipidomicsR_0.3.6.tgz(r-4.5-any)
LipidomicsR_0.3.6.tar.gz(r-4.7-any)LipidomicsR_0.3.6.tar.gz(r-4.6-any)
LipidomicsR_0.3.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
LipidomicsR/json (API)

# Install 'LipidomicsR' in R:

install.packages('LipidomicsR', repos = c('https://mingshi1.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mingshi1/lipidomicsr/issues

On CRAN:

3.00 score 2 stars 1 scripts 143 downloads 19 exports 176 dependencies

Last updated from:8efb7db17d. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	209
source / vignettes	OK	236
linux-release-x86_64	NOTE	203
macos-release-arm64	NOTE	150
macos-oldrel-arm64	NOTE	164
windows-devel	NOTE	168
windows-release	NOTE	183
windows-oldrel	NOTE	127
wasm-release	OK	158

Exports:abundance.lineplot abundance.plot abundance.signif abundance.summary channel.delete delRep FC_P groupXpert heatmap importer noridx normalization_calculator plotRadar QCplot replicate.delete rsd_calculator sepclass total.abundance volcano

Dependencies:abind askpass backports base64enc bit bit64 blob boot broom bslib cachem callr car carData cellranger class cli clipr codetools coin colorspace conflicted cowplot cpp11 crayon curl data.table DBI dbplyr Deriv DescTools digest doBy dplyr dtplyr e1071 evaluate Exact expm farver fastmap fmsb fontawesome fontBitstreamVera fontLiberation fontquiver forcats forecast Formula fracdiff fs gargle gdtools generics ggforce ggiraph ggplot2 ggplotify ggrepel ggsci gld glue googledrive googlesheets4 gridGraphics gtable haven highr hms htmltools htmlwidgets httr ids isoband jquerylib jsonlite knitr labeling lattice libcoin lifecycle lme4 lmom lmtest lubridate magrittr MASS Matrix MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr modeltools multcomp multcompView mvtnorm nlme nloptr nnet nortest numDeriv openssl otel pbkrtest pheatmap pillar pkgconfig plyr polyclip prettyunits processx progress proxy ps purrr quantreg R6 ragg rappdirs rbibutils RColorBrewer rcompanion Rcpp RcppArmadillo RcppEigen Rdpack readr readxl reformulas rematch rematch2 reprex reshape2 rlang rmarkdown rootSolve rstudioapi rvest S7 sandwich sass scales selectr SparseM stringi stringr survival sys systemfonts textshaping TH.data tibble tidyr tidyselect tidyverse timechange timeDate tinytex tweenr tzdb urca utf8 uuid vctrs viridisLite vroom withr xfun xml2 yaml yulab.utils zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
absolute.calculator()	absolute.calculator
Plot Abundance Data	abundance.lineplot
Plot Abundance Data	abundance.plot
Analyze Abundance Significance	abundance.signif
Summarize Abundance Data	abundance.summary
Delete repeated channel data generated by LC-MS	channel.delete
delRep()	delRep
Calculate Fold Change and p-values for differential expression analysis	FC_P
groupXpert()	groupXpert
heatmap()	heatmap
importer()	importer
lEa()	lEa
lEr	lEr
Global environment settings of LipidomicsR	lipidomicsR_env
nor.absolute()	nor.absolute
nor.relative()	nor.relative
noridx()	noridx
normalization_calculator()	normalization_calculator
percent.calculator()	percent.calculator
plotRadar()	plotRadar
QCplot()	QCplot
relative.calculator()	relative_calculator
Delete repeated channel data generated by LC-MS	replicate.delete
Calculate Relative Standard Deviation (RSD)	rsd_calculator
sepclass()	sepclass
toGroup.calculator()	toGroup.calculator
Calculate Total Abundance Data	total.abundance
Generate Volcano Plot	volcano