Package: SDAMS 1.27.0

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_1.27.0.tar.gz
SDAMS_1.27.0.zip(r-4.5)SDAMS_1.27.0.zip(r-4.4)SDAMS_1.27.0.zip(r-4.3)
SDAMS_1.27.0.tgz(r-4.4-any)SDAMS_1.27.0.tgz(r-4.3-any)
SDAMS_1.27.0.tar.gz(r-4.5-noble)SDAMS_1.27.0.tar.gz(r-4.4-noble)
SDAMS_1.27.0.tgz(r-4.4-emscripten)SDAMS_1.27.0.tgz(r-4.3-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-1.27.0(bioc 3.21)SDAMS-1.26.0(bioc 3.20)

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 192 downloads 2 mentions 3 exports 61 dependencies

Last updated 2 months agofrom:faef9bc609. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	NOTE	Dec 19 2024
R-4.5-linux	NOTE	Dec 19 2024
R-4.4-win	NOTE	Dec 19 2024
R-4.4-mac	NOTE	Dec 19 2024
R-4.3-win	NOTE	Dec 19 2024
R-4.3-mac	NOTE	Dec 19 2024

Exports:createSEFromCSV createSEFromMatrix SDA

Dependencies:abind askpass Biobase BiocGenerics cli colorspace crayon curl DelayedArray fansi farver generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig plyr qvalue R6 RColorBrewer Rcpp reshape2 rlang S4Arrays S4Vectors scales SparseArray stringi stringr SummarizedExperiment sys tibble trust UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

SDAMS Vignette

Rendered fromSDAMS.Rnwusingutils::Sweaveon Dec 19 2024.

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