SDAMS
This is the released version of SDAMS; for the devel version, see SDAMS.
Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data
Bioconductor version: Release (3.23)
This Package utilizes a Semi-parametric Differential Abundance/expression analysis (SDA) method for metabolomics and proteomics data from mass spectrometry as well as single-cell RNA sequencing data. SDA is able to robustly handle non-normally distributed data and provides a clear quantification of the effect size.
Author: Yuntong Li <liyuntong0704 at gmail.com>, Chi Wang <chi.wang at uky.edu>, Li Chen <lichenuky at uky.edu>
Maintainer: Yuntong Li <liyuntong0704 at gmail.com>
citation("SDAMS")):
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")
BiocManager::install("SDAMS")
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("SDAMS")| SDAMS Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, MassSpectrometry, Metabolomics, Proteomics, SingleCell, Software |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | GPL |
| Depends | R (>= 3.5), SummarizedExperiment |
| Imports | trust, qvalue, methods, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | testthat |
| Linking To | |
| 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 | SDAMS_1.32.0.tar.gz |
| Windows Binary (x86_64) | SDAMS_1.32.0.zip |
| macOS Binary (big-sur-x86_64) | SDAMS_1.32.0.tgz |
| macOS Binary (sonoma-arm64) | SDAMS_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SDAMS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SDAMS |
| Bioc Package Browser | https://code.bioconductor.org/browse/SDAMS/ |
| Package Short Url | https://bioconductor.org/packages/SDAMS/ |
| Package Downloads Report | Download Stats |