DEqMS
DEqMS is a statistical method for analyzing differential protein expression in mass spectrometry data. DEqMS considers the dependence of variance on the number of peptide-spectrum matches (PSMs) or peptides used for protein quantification. This feature allows for a more accurate estimation of protein variance and enables the inclusion of single peptide identifications without increasing false discoveries.
Topic
Proteomics;Proteomics experiment;Small molecules;Sequence analysis;Protein expression
Detail
Operation: Label-free quantification;TMT-tag;Differential protein expression analysis;iTRAQ;Expression analysis
Software interface: Library
Language: R
License: GNU Lesser General Public License v3.0
Cost: Free
Version name: 1.20.0
Credit: -
Input: -
Output: -
Contact: Yafeng Zhu yafeng.zhu@outlook.com
Collection: -
Maturity: Stable
Publications
- DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis.
- Zhu Y, et al. DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis. DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis. 2020; 19:1047-1057. doi: 10.1074/mcp.TIR119.001646
- https://doi.org/10.1074/MCP.TIR119.001646
- PMID: 32205417
- PMC: PMC7261819
Download and documentation
Source: https://bioconductor.org/packages/release/bioc/src/contrib/DEqMS_1.20.0.tar.gz
Documentation: https://bioconductor.org/packages/release/bioc/manuals/DEqMS/man/DEqMS.pdf
Home page: https://bioconductor.org/packages/release/bioc/html/DEqMS.html
Links: https://bioconductor.org/packages/release/bioc/vignettes/DEqMS/inst/doc/DEqMS-package-vignette.html
Links: https://bioconductor.org/packages/release/bioc/vignettes/DEqMS/inst/doc/DEqMS-package-vignette.R
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