sfi
This is the development version of sfi; for the stable release version, see sfi.
Data analysis for Single File Injections (SFIs) mode LC-MS analysis
DOI: 10.18129/B9.bioc.sfi
Bioconductor version: Development (3.24)
Data analysis for Single File Injections(SFIs) mode LC-MS analysis. In SFIs mode, pooled samples are initially injected to serve as reference peaks for subsequent analyses. Repeated injections of individual samples are then performed at fixed time intervals using isocratic elution. This package provides the functions to analyze data from SFIs mode including peak picking and peak reassignment.
Maintainer: Miao YU <yufreecas at gmail.com>
citation("sfi")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("sfi")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("sfi")| sfi workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FeatureExtraction, MassSpectrometry, Metabolomics, Software |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | Rcpp, enviGCMS, stats, mzR, rmarkdown, methods, SummarizedExperiment, S4Vectors |
| System Requirements | |
| URL | https://github.com/yufree/sfi |
| Bug Reports | https://github.com/yufree/sfi/issues/new |
See More
| Suggests | knitr, data.table, BiocStyle, ggplot2, MsCoreUtils, testthat (>= 3.0.0) |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | sfi_1.1.0.tar.gz |
| Windows Binary (x86_64) | sfi_1.1.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | sfi_1.1.0.tgz |
| macOS Binary (sonoma-arm64) | sfi_1.1.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sfi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sfi |
| Bioc Package Browser | https://code.bioconductor.org/browse/sfi/ |
| Package Short Url | https://bioconductor.org/packages/sfi/ |
| Package Downloads Report | Download Stats |