Package: FAMetA 0.1.6

FAMetA: Fatty Acid Metabolic Analysis

Fatty acid metabolic analysis aimed to the estimation of FA import (I), de novo synthesis (S), fractional contribution of the 13C-tracers (D0, D1, D2), elongation (E) and desaturation (Des) based on mass isotopologue data.

Authors:Maribel Alcoriza-Balaguer [aut, cre], Juan Carlos Garcia-Cañaveras [ctb], Agustin Lahoz [ths]

FAMetA_0.1.6.tar.gz
FAMetA_0.1.6.zip(r-4.7)FAMetA_0.1.6.zip(r-4.6)FAMetA_0.1.6.zip(r-4.5)
FAMetA_0.1.6.tgz(r-4.6-any)FAMetA_0.1.6.tgz(r-4.5-any)
FAMetA_0.1.6.tar.gz(r-4.7-any)FAMetA_0.1.6.tar.gz(r-4.6-any)
FAMetA_0.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
FAMetA/json (API)

# Install 'FAMetA' in R:

install.packages('FAMetA', repos = c('https://maialba3.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/maialba3/fameta/issues

Datasets:

desaturationsdb - Desaturation reactions database.
examplefadata - Example fadata list.
fattyacidsdb - Fatty Acids database.
parameters - Parameters for FA metabolic analysis.
ssexamplefadata - Toy example fadata list.

On CRAN:

3.70 score 1 stars 3 scripts 274 downloads 18 exports 96 dependencies

Last updated from:4e3101dc33. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	164
source / vignettes	OK	206
linux-release-x86_64	NOTE	210
macos-release-arm64	NOTE	235
macos-oldrel-arm64	NOTE	205
windows-devel	NOTE	129
windows-release	NOTE	106
windows-oldrel	NOTE	103
wasm-release	OK	125

Exports:addFA annotateFA blankSubstraction changeFArt correctNatAb13C curateFAannotations dataCorrection desaturationAnalysis elongationAnalysis externalNormalization normalizeIS plotFA readfadatafile removeFA searchFAisotopes searchIS summarizeResults synthesisAnalysis

Dependencies:accucor base64enc bit bit64 bitops bslib cachem caTools cellranger CHNOSZ cli clipr codetools cpp11 crayon crosstalk digest dplyr DT evaluate farver fastmap fontawesome fs future future.apply generics ggplot2 globals glue gplots gtable gtools highr hms htmltools htmlwidgets isoband iterators jquerylib jsonlite KernSmooth knitr labeling later lazyeval lifecycle LipidMS listenv magrittr memoise mime minpack.lm nnls otel parallelly patchwork pillar pkgconfig plyr prettyunits progress promises purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp readMzXmlData readr readxl rematch rlang rmarkdown S7 sass scales stringi stringr tibble tidyr tidyselect tinytex tzdb utf8 vctrs viridisLite vroom withr writexl xfun XML yaml

FAMetA workflow

Rendered fromvignette.Rmdusingknitr::rmarkdown

Last update: 2021-11-18
Started: 2021-11-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add missing FA annotations	addFA
FA annotation	annotateFA
substract blank samples.	blankSubstraction
Modify rt peak limits of annotated FAs	changeFArt
correct data for natural abundance of 13C using accucor algorithm.	correctNatAb13C
Modify FA annotations	curateFAannotations
Data correction for natural abundance of 13C and data normalization using internal standards followed by blank substraction.	dataCorrection
Desaturation analysis of fatty acids.	desaturationAnalysis
Desaturation reactions database.	desaturationsdb
Elongation analysis of fatty acids longer than 16 carbons.	elongationAnalysis
Example fadata list.	examplefadata
External normalization using additional measures (i.e. protein levels).	externalNormalization
Fatty Acids database.	fattyacidsdb
Data normalization using internal stardards.	normalizeIS
Parameters for FA metabolic analysis.	parameters
Plot FA EICs	plotFA
read FA data from a csv file.	readfadatafile
Remove incorrect FA annotations	removeFA
Search FA isotopes	searchFAisotopes
Search internal stardards.	searchIS
Toy example fadata list.	ssexamplefadata
Obtain result tables and heatmaps that help interpreting your results.	summarizeResults
De novo synthesis analysis of fatty acids until 16 carbons.	synthesisAnalysis