| 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 |
