Package: ProteoMM 1.23.0

Yuliya V Karpievitch

ProteoMM: Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform

ProteoMM is a statistical method to perform model-based peptide-level differential expression analysis of single or multiple datasets. For multiple datasets ProteoMM produces a single fold change and p-value for each protein across multiple datasets. ProteoMM provides functionality for normalization, missing value imputation and differential expression. Model-based peptide-level imputation and differential expression analysis component of package follows the analysis described in “A statistical framework for protein quantitation in bottom-up MS based proteomics" (Karpievitch et al. Bioinformatics 2009). EigenMS normalisation is implemented as described in "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition." (Karpievitch et al. Bioinformatics 2009).

Authors:Yuliya V Karpievitch, Tim Stuart and Sufyaan Mohamed

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NEWS

# Install 'ProteoMM' in R:
install.packages('ProteoMM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • hs_peptides - Hs_peptides - peptide-level intensities for human
  • mm_peptides - Mm_peptides - peptide-level intensities for mouse

On BioConductor:ProteoMM-1.23.0(bioc 3.20)ProteoMM-1.22.0(bioc 3.19)

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

bioconductor-package

18 exports 0.82 score 82 dependencies

Last updated 2 months agofrom:0473b9a7c7

Exports:convert_log2eig_norm1eig_norm2eigen_pig.testget_presAbs_protsmake_intencitiesmake_metamakeLMFormulaMBimputepeptideLevel_DEpeptideLevel_PresAbsDEplot_3_pep_trends_NOfileplot_volcanoplot_volcano_wLabprot_level_multi_partprot_level_multiMat_PresAbssubset_proteins

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIdbplyrdigestdplyrfansifarverfastmapfilelockgdatagenericsGenomeInfoDbGenomeInfoDbDataggplot2ggrepelgluegtablegtoolshmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcpprlangRSQLiteS4VectorsscalesstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrxml2XVectorzlibbioc

ProteoMM - Multi-Dataset Model-based Differential Expression Proteomics Platform

Yuliya V Karpievitch, Tim Stuart, Sufyaan Mohamed

Rendered fromProteoMM_vignette.Rmdusingknitr::knitron Jul 01 2024.

Last update: 2018-10-09
Started: 2018-10-09