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-4.5)FAMetA_0.1.6.zip(r-4.4)FAMetA_0.1.6.zip(r-4.3)
FAMetA_0.1.6.tgz(r-4.4-any)FAMetA_0.1.6.tgz(r-4.3-any)
FAMetA_0.1.6.tar.gz(r-4.5-noble)FAMetA_0.1.6.tar.gz(r-4.4-noble)
FAMetA_0.1.6.tgz(r-4.4-emscripten)FAMetA_0.1.6.tgz(r-4.3-emscripten)
FAMetA.pdf |FAMetA.html✨
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 2 scripts 277 downloads 18 exports 89 dependencies

Last updated 9 months agofrom:4e3101dc33. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 01 2024
R-4.5-win	NOTE	Nov 01 2024
R-4.5-linux	NOTE	Nov 01 2024
R-4.4-win	OK	Nov 01 2024
R-4.4-mac	OK	Nov 01 2024
R-4.3-win	OK	Nov 01 2024
R-4.3-mac	OK	Nov 01 2024

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 colorspace commonmark cpp11 crayon digest doParallel dplyr evaluate fansi farver fastmap fontawesome foreach fs generics glue gplots gtools highr hms htmltools httpuv iterators jquerylib jsonlite KernSmooth knitr labeling later lifecycle LipidMS magrittr memoise mime minpack.lm munsell nnls pillar pkgconfig plyr prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp readMzXmlData readr readxl rematch rlang rmarkdown sass scales shiny shinythemes sourcetools stringi stringr tibble tidyr tidyselect tinytex tzdb utf8 vctrs viridisLite vroom withr writexl xfun XML xtable yaml

FAMetA workflow

Rendered fromvignette.Rmdusingknitr::rmarkdownon Nov 01 2024.

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