Package: SDAMS 1.31.0

Yuntong Li

SDAMS: Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data

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.

Authors:Yuntong Li <[email protected]>, Chi Wang <[email protected]>, Li Chen <[email protected]>

SDAMS_1.31.0.tar.gz
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SDAMS_1.31.0.tgz(r-4.5-emscripten)
SDAMS.pdf |SDAMS.html✨
SDAMS/json (API)
NEWS

# Install 'SDAMS' in R:

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

Datasets:

exampleSingleCell - Two example datasets for SDAMS package
exampleSumExp - Two example datasets for SDAMS package

On BioConductor:SDAMS-1.31.0(bioc 3.23)SDAMS-1.30.0(bioc 3.22)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology differentialexpression metabolomics proteomics massspectrometry singlecell

3.60 score 1 scripts 345 downloads 2 mentions 3 exports 42 dependencies

Last updated from:b82dfb11e5. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	172
linux-devel-x86_64	NOTE	286
source / vignettes	OK	243
linux-release-x86_64	NOTE	292
macos-release-arm64	NOTE	154
macos-oldrel-arm64	NOTE	199
windows-devel	NOTE	237
windows-release	NOTE	235
windows-oldrel	NOTE	236
wasm-release	OK	116

Exports:createSEFromCSV createSEFromMatrix SDA

Dependencies:abind Biobase BiocGenerics cli cpp11 DelayedArray farver generics GenomicRanges ggplot2 glue gtable IRanges isoband labeling lattice lifecycle magrittr Matrix MatrixGenerics matrixStats plyr qvalue R6 RColorBrewer Rcpp reshape2 rlang S4Arrays S4Vectors S7 scales Seqinfo SparseArray stringi stringr SummarizedExperiment trust vctrs viridisLite withr XVector

SDAMS Vignette

Rendered fromSDAMS.Rnwusingutils::Sweaveon Apr 04 2026.

Last update: 2023-07-26
Started: 2018-02-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
SDAMS package for differential abundance/expression analysis of Metabolomics, Proteomics and single-cell RNA sequencing data	SDAMS-package
Mass spectrometry data input	createSEFromCSV createSEFromMatrix dataInput
Two example datasets for SDAMS package	exampleData exampleSingleCell exampleSumExp
Semi-parametric differential abuandance/expression analysis	SDA