现在Bioconductor version 3.11中有 132个 蛋白质组学 和 88个 质谱包 。其它的非Bioconductor包在
r Biocexptpkg("RforProteomics")中有介绍，用R打开RforProteomics()或者在线阅读。
R包太多了自己慢慢看、慢慢试用！！！
132个蛋白质组学包，大部分都没有用过😝，保存备查。
| Package | Title | Version | |
|---|---|---|---|
| artMS | artMS | Analytical R tools for Mass Spectrometry | 1.5.0 |
| ASEB | ASEB | Predict Acetylated Lysine Sites | 1.31.0 |
| AssessORF | AssessORF | Assess Gene Predictions Using Proteomics and Evolutionary Conservation | 1.5.0 |
| bioassayR | bioassayR | Cross-target analysis of small molecule bioactivity | 1.25.0 |
| biobroom | biobroom | Turn Bioconductor objects into tidy data frames | 1.19.0 |
| BioNetStat | BioNetStat | Biological Network Analysis | 1.7.0 |
| biosigner | biosigner | Signature discovery from omics data | 1.15.0 |
| BRAIN | BRAIN | Baffling Recursive Algorithm for Isotope distributioN calculations | 1.33.0 |
| calm | calm | Covariate Assisted Large-scale Multiple testing | 1.1.0 |
| Cardinal | Cardinal | A mass spectrometry imaging toolbox for statistical analysis | 2.5.0 |
| CausalR | CausalR | Causal network analysis methods | 1.19.0 |
| CellNOptR | CellNOptR | Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data | 1.33.0 |
| ChemmineOB | ChemmineOB | R interface to a subset of OpenBabel functionalities | 1.25.0 |
| ChemmineR | ChemmineR | Cheminformatics Toolkit for R | 3.39.0 |
| cisPath | cisPath | Visualization and management of the protein-protein interaction networks. | 1.27.0 |
| cleaver | cleaver | Cleavage of Polypeptide Sequences | 1.25.0 |
| clippda | clippda | A package for the clinical proteomic profiling data analysis | 1.37.0 |
| CNORdt | CNORdt | Add-on to CellNOptR: Discretized time treatments | 1.29.0 |
| CNORfeeder | CNORfeeder | Integration of CellNOptR to add missing links | 1.27.0 |
| CNORode | CNORode | ODE add-on to CellNOptR | 1.29.0 |
| customProDB | customProDB | Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search | 1.27.0 |
| cydar | cydar | Using Mass Cytometry for Differential Abundance Analyses | 1.11.0 |
| DAPAR | DAPAR | Tools for the Differential Analysis of Proteins Abundance with R | 1.19.0 |
| deco | deco | Decomposing Heterogeneous Cohorts using Omic Data Profiling | 1.3.0 |
| deltaGseg | deltaGseg | deltaGseg | 1.27.0 |
| DEP | DEP | Differential Enrichment analysis of Proteomics data | 1.9.0 |
| DEqMS | DEqMS | a tool to perform statistical analysis of differential protein expression for quantitative proteomics data. | 1.5.0 |
| diffcyt | diffcyt | Differential discovery in high-dimensional cytometry via high-resolution clustering | 1.7.0 |
| DominoEffect | DominoEffect | Identification and Annotation of Protein Hotspot Residues | 1.7.0 |
| Doscheda | Doscheda | A DownStream Chemo-Proteomics Analysis Pipeline | 1.9.0 |
| drawProteins | drawProteins | Package to Draw Protein Schematics from Uniprot API output | 1.7.0 |
| EGSEA | EGSEA | Ensemble of Gene Set Enrichment Analyses | 1.15.0 |
| eiR | eiR | Accelerated similarity searching of small molecules | 1.27.0 |
| fCI | fCI | f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics | 1.17.0 |
| fmcsR | fmcsR | Mismatch Tolerant Maximum Common Substructure Searching | 1.29.0 |
| GraphPAC | GraphPAC | Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach. | 1.29.0 |
| HPAanalyze | HPAanalyze | Retrieve and analyze data from the Human Protein Atlas | 1.5.0 |
| hpar | hpar | Human Protein Atlas in R | 1.29.0 |
| IMMAN | IMMAN | Interlog protein network reconstruction by Mapping and Mining ANalysis | 1.7.0 |
| InterMineR | InterMineR | R Interface with InterMine-Powered Databases | 1.9.0 |
| iPAC | iPAC | Identification of Protein Amino acid Clustering | 1.31.0 |
| IPPD | IPPD | Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching | 1.35.0 |
| isobar | isobar | Analysis and quantitation of isobarically tagged MSMS proteomics data | 1.33.0 |
| kimod | kimod | A k-tables approach to integrate multiple Omics-Data | 1.15.0 |
| KinSwingR | KinSwingR | KinSwingR: network-based kinase activity prediction | 1.5.0 |
| KnowSeq | KnowSeq | A R package to extract knowledge by using RNA-seq raw files | 1.1.0 |
| limma | limma | Linear Models for Microarray Data | 3.43.0 |
| LPEadj | LPEadj | A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size. | 1.47.0 |
| MassSpecWavelet | MassSpecWavelet | Mass spectrum processing by wavelet-based algorithms | 1.53.0 |
| mixOmics | mixOmics | Omics Data Integration Project | 6.11.0 |
| MSGFgui | MSGFgui | A shiny GUI for MSGFplus | 1.21.0 |
| MSGFplus | MSGFplus | An interface between R and MS-GF+ | 1.21.0 |
| msmsEDA | msmsEDA | Exploratory Data Analysis of LC-MS/MS data by spectral counts | 1.25.0 |
| msmsTests | msmsTests | LC-MS/MS Differential Expression Tests | 1.25.0 |
| MSnbase | MSnbase | Base Functions and Classes for Mass Spectrometry and Proteomics | 2.13.0 |
| MSnID | MSnID | Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications | 1.21.0 |
| MSstats | MSstats | Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments | 3.19.0 |
| MSstatsQC | MSstatsQC | Longitudinal system suitability monitoring and quality control for proteomic experiments | 2.5.0 |
| MSstatsQCgui | MSstatsQCgui | A graphical user interface for MSstatsQC package | 1.7.0 |
| MSstatsSampleSize | MSstatsSampleSize | Simulation tool for optimal design of high-dimensional MS-based proteomics experiment | 1.1.0 |
| MSstatsTMT | MSstatsTMT | Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling | 1.5.0 |
| mzID | mzID | An mzIdentML parser for R | 1.25.0 |
| mzR | mzR | parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data) | 2.21.0 |
| NormalyzerDE | NormalyzerDE | Evaluation of normalization methods and calculation of differential expression analysis statistics | 1.5.0 |
| omicRexposome | omicRexposome | Exposome and omic data associatin and integration analysis | 1.9.0 |
| OmicsLonDA | OmicsLonDA | Omics Longitudinal Differential Analysis | 1.1.0 |
| oppti | oppti | Outlier Protein and Phosphosite Target Identifier | 1.1.0 |
| PAA | PAA | PAA (Protein Array Analyzer) | 1.21.0 |
| Path2PPI | Path2PPI | Prediction of pathway-related protein-protein interaction networks | 1.17.0 |
| pathview | pathview | a tool set for pathway based data integration and visualization | 1.27.0 |
| pathwayPCA | pathwayPCA | Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection | 1.3.0 |
| PCpheno | PCpheno | Phenotypes and cellular organizational units | 1.49.0 |
| PECA | PECA | Probe-level Expression Change Averaging | 1.23.0 |
| pepXMLTab | pepXMLTab | Parsing pepXML files and filter based on peptide FDR. | 1.21.0 |
| PGA | PGA | An package for identification of novel peptides by customized database derived from RNA-Seq | 1.17.0 |
| pgca | pgca | PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data | 1.11.0 |
| phosphonormalizer | phosphonormalizer | Compensates for the bias introduced by median normalization in phosphoproteomics | 1.11.0 |
| plgem | plgem | Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM) | 1.59.0 |
| PLPE | PLPE | Local Pooled Error Test for Differential Expression with Paired High-throughput Data | 1.47.0 |
| PowerExplorer | PowerExplorer | Power Estimation Tool for RNA-Seq and proteomics data | 1.7.0 |
| ppiStats | ppiStats | Protein-Protein Interaction Statistical Package | 1.53.0 |
| PrInCE | PrInCE | Predicting Interactomes from Co-Elution | 1.3.0 |
| proBAMr | proBAMr | Generating SAM file for PSMs in shotgun proteomics data | 1.21.0 |
| proBatch | proBatch | Tools for Diagnostics and Corrections of Batch Effects in Proteomics | 1.3.0 |
| PROcess | PROcess | Ciphergen SELDI-TOF Processing | 1.63.0 |
| procoil | procoil | Prediction of Oligomerization of Coiled Coil Proteins | 2.15.0 |
| proFIA | proFIA | Preprocessing of FIA-HRMS data | 1.13.0 |
| pRoloc | pRoloc | A unifying bioinformatics framework for spatial proteomics | 1.27.0 |
| pRolocGUI | pRolocGUI | Interactive visualisation of spatial proteomics data | 1.21.0 |
| ProteomicsAnnotationHubData | ProteomicsAnnotationHubData | Transform public proteomics data resources into Bioconductor Data Structures | 1.17.0 |
| ProteoMM | ProteoMM | Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform | 1.5.0 |
| ProtGenerics | ProtGenerics | S4 generic functions for Bioconductor proteomics infrastructure | 1.19.0 |
| pulsedSilac | pulsedSilac | Analysis of pulsed-SILAC quantitative proteomics data | 1.1.0 |
| Pviz | Pviz | Peptide Annotation and Data Visualization using Gviz | 1.21.0 |
| qcmetrics | qcmetrics | A Framework for Quality Control | 1.25.0 |
| qPLEXanalyzer | qPLEXanalyzer | Tools for qPLEX-RIME data analysis | 1.5.0 |
| QuartPAC | QuartPAC | Identification of mutational clusters in protein quaternary structures. | 1.19.0 |
| rain | rain | Rhythmicity Analysis Incorporating Non-parametric Methods | 1.21.0 |
| RankProd | RankProd | Rank Product method for identifying differentially expressed genes with application in meta-analysis | 3.13.0 |
| RCASPAR | RCASPAR | A package for survival time prediction based on a piecewise baseline hazard Cox regression model. | 1.33.0 |
| Rcpi | Rcpi | Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery | 1.23.0 |
| ReactomeGSA | ReactomeGSA | Client for the Reactome Analysis Service for comparative multi-omics gene set analysis | 1.1.0 |
| ropls | ropls | PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data | 1.19.0 |
| RpsiXML | RpsiXML | R interface to PSI-MI 2.5 files | 2.29.0 |
| rpx | rpx | R Interface to the ProteomeXchange Repository | 1.23.0 |
| rScudo | rScudo | Signature-based Clustering for Diagnostic Purposes | 1.3.0 |
| rTANDEM | rTANDEM | Interfaces the tandem protein identification algorithm in R | 1.27.0 |
| sapFinder | sapFinder | A package for variant peptides detection and visualization in shotgun proteomics. | 1.25.0 |
| SBGNview | SBGNview | Overlay omics data onto SBGN pathway diagram | 1.1.0 |
| ScISI | ScISI | In Silico Interactome | 1.59.0 |
| SDAMS | SDAMS | Differential Abundant Analysis for Metabolomics and Proteomics Data | 1.7.0 |
| shinyTANDEM | shinyTANDEM | Provides a GUI for rTANDEM | 1.25.0 |
| SLGI | SLGI | Synthetic Lethal Genetic Interaction | 1.47.0 |
| SMAD | SMAD | Statistical Modelling of AP-MS Data (SMAD) | 1.3.0 |
| SpacePAC | SpacePAC | Identification of Mutational Clusters in 3D Protein Space via Simulation. | 1.25.0 |
| sparsenetgls | sparsenetgls | Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression | 1.5.0 |
| statTarget | statTarget | Statistical Analysis of Molecular Profiles | 1.17.0 |
| SubCellBarCode | SubCellBarCode | SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome | 1.3.0 |
| SWATH2stats | SWATH2stats | Transform and Filter SWATH Data for Statistical Packages | 1.17.0 |
| synapter | synapter | Label-free data analysis pipeline for optimal identification and quantitation | 2.11.0 |
| tofsims | tofsims | Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data | 1.15.0 |
| TPP | TPP | Analyze thermal proteome profiling (TPP) experiments | 3.15.0 |
| TPP2D | TPP2D | FDR-controlled analysis of 2D-TPP experiments | 1.3.0 |
| XINA | XINA | Multiplexes isobaric mass tagged-based kinetics data for network analysis | 1.5.0 |
| proteoQC | proteoQC | An R package for proteomics data quality control | 1.23.0 |
| specL | specL | specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics | 1.21.0 |
| ROTS | ROTS | Reproducibility-Optimized Test Statistic | 1.15.0 |
| readat | readat | Functionality to Read and Manipulate SomaLogic ADAT files | 1.13.0 |
| topdownr | topdownr | Investigation of Fragmentation Conditions in Top-Down Proteomics | 1.9.0 |
| phemd | phemd | Phenotypic EMD for comparison of single-cell samples | 1.3.0 |
| proDA | proDA | Differential Abundance Analysis of Label-Free Mass Spectrometry Data | 1.1.0 |
| MBQN | MBQN | Mean/Median-balanced quantile normalization | 1.1.0 |
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