Biocview "Proteomics"

A bioconductor package for exploration of alignment gap positions from RNA-seq data

Accelerated similarity searching of small molecules

A collection of tools for imaging MS data processing

A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.

Add-on to CellNOptR: Discretized time treatments

A DownStream Chemo-Proteomics Analysis Pipeline

A Framework for Quality Control

A graphical user interface for MSstatsQC package

A k-tables approach to integrate multiple Omics-Data

A mass spectrometry imaging toolbox for statistical analysis

Analysis and quantitation of isobarically tagged MSMS proteomics data

Analysis of pulsed-SILAC quantitative proteomics data

Analytical R tools for Mass Spectrometry

Analyze thermal proteome profiling (TPP) experiments

An implementation of the Search All, Asses Subset strategy for FDR estimation shotgun proteomics.

An interface between R and MS-GF+

An mzIdentML parser for R

An package for identification of novel peptides by customized database derived from RNA-Seq

An R package for proteomics data quality control

An R package for the Bayesian analysis of differential subcellular localisation experiments

A package for survival time prediction based on a piecewise baseline hazard Cox regression model.

A package for the clinical proteomic profiling data analysis

A package for variant peptides detection and visualization in shotgun proteomics.

A Pipeline Manager

A set of methods and tools for comprehensive analysis of phosphoproteomics data

A shiny GUI for MSGFplus

Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

Assessment of apoptosis and necroptosus unsing proteomics

A tool for large scale omics datasets evaluation

a tool set for pathway based data integration and visualization

a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions

A unifying bioinformatics framework for spatial proteomics

Baffling Recursive Algorithm for Isotope distributioN calculations

Base Functions and Classes for Mass Spectrometry and Proteomics

Base NanoString Experiment Class

Bioc2014 workshop on R / Bioconductor packages for Proteomics

Biological Network Analysis

BraDiPluS - Braille Display Plugs Data Analysis

Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful

Causal network analysis methods

Cheminformatics Toolkit for R

Ciphergen SELDI-TOF Processing

Cleavage of Polypeptide Sequences

Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

Compensates for the bias introduced by median normalization in phosphoproteomics. This is done by taking enriched and non-enriched data and creating a normalization factor.

Complex feature detection using SEC protein chromatograms.

Complexome Profiling Analysis package

Compute constrained proportional assignments for fractionated protein abundance

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Conversion between the Workflow4metabolomics tabulated format and the ExpressionSet bioconductor class

Core Utils for Mass Spectrometry Data

COSMOS (Causal Oriented Search of Multi-Omic Space)

Covariate Assisted Large-scale Multiple testing

Cross-target analysis of small molecule bioactivity

Data Independent Acquisition Library Editing to Convert The Species

Data normalization by matrix raking

Decomposing Heterogeneous Cohorts using Omic Data Profiling

deltaGseg

Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)

Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)

Diagnostic Plots to Evaluate the Target Decoy Approach

Differential Abundance Analysis of Label-Free Mass Spectrometry Data

Differential abundance analysis with a right censored covariate in high-dimensional cytometry

Differential Abundant Analysis for Metabolomics and Proteomics Data

Differential Abundant Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data

Differential discovery in high-dimensional cytometry via high-resolution clustering

Differential Enrichment analysis of Proteomics data

Differential expression using kernel-based score test

Diffusion scores on biological networks

Direct Access to Orbitrap Data and Beyond

Downstream analysis of the MaxQuant output

Drug-Target Interactions

Dynamic Programming Based Alignment of MS2 Chromatograms

Effective mobility scale transformation of CE-MS(/MS) data

Encapsulate X!Tandem in R.

Ensemble of Gene Set Enrichment Analyses

Estimation of protein distribution from quantitative subcellular fractionation experiments using a constrained proportional assignment model

Evaluation of normalization methods and calculation of differential expression analysis statistics

EWCE for Multiple Gene Lists

Exploratory Data Analysis of LC-MS/MS data by spectral counts

Exposome and omic data associatin and integration analysis

Expression Weighted Celltype Enrichment

f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics

FDR-controlled analysis of 2D-TPP experiments with replicates

FDR-controlled analysis of SPP experiments

Finding the DNA and protein sequences in a list of genomic or proteomic loci

Finding the DNA and Protein Sequences of Any Genomic or Proteomic Loci

flexible pipelines for secretome prediction

Functionality to Read and Manipulate SomaLogic ADAT files

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Generate customized protein databases from NGS data for proteomics search

Generating Protein Sequences with Deep Generative Models

Generating SAM file for PSMs in shotgun proteomics data

Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

Generic infrastructure for Bioconductor mass spectrometry packages

Genetic inteRaction and EssenTiality neTwork mApper

Handling and Managing Peptide Spectrum Matches

High throughput prioritized acquisition and processing of tandem mass spectra

Host-Pathogen Interaction Prediction

Human Protein Atlas in R

Identification and Annotation of Protein Hotspot Residues

Identification of Mutational Clusters in 3D Protein Space via Simulation.

Identification of mutational clusters in protein quaternary structures.

Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.

Identification of Protein Amino acid Clustering

Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

Imputation of label-free mass spectrometry peptides

Infrastructure for Chromatographic Mass Spectrometry Data

Infrastructure for Ion Mobility enabled mass spectrometry

Infrastructure for Mass Spectrometry Experiments

In Silico Interactome

Integration of CellNOptR to add missing links

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Interactive visualisation of spatial proteomics data

Interfaces the tandem protein identification algorithm in R

Interlog protein network reconstruction by Mapping and Mining ANalysis

Investigation of Fragmentation Conditions in Top-Down Proteomics

Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching

KinSwingR: network-based kinase activity prediction

Label-free data analysis pipeline for optimal identification and quantitation

LC-MS/MS Differential Expression Tests

Linear Models for Microarray Data

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Local Pooled Error Test for Differential Expression with Paired High-throughput Data

Longitudinal system suitability monitoring and quality control for proteomic experiments

Managing amino acid modifications for mass spectrometry

Manipulating and exploring protein and proteomics data

Marker Enrichment Modeling (MEM)

MassQL support for Spectra

Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Mass spectrometry data backend

Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files

Mass Spectrometry Data Backend for NIST msp Files

Mass spectrometry data backends for The Human Metabolome Database

Mass spectrum processing by wavelet-based algorithms

Mean/Median-balanced quantile normalization

Minimal Protein Set Explaining Peptide Spectrum Matches

Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

Mismatch Tolerant Maximum Common Substructure Searching

Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

MsQuality - Quality metric calculation from Spectra and MsExperiment objects

Multi-Contrast Gene Set Enrichment Analysis

Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform

Multilevel Model for Multivariate Responses with Missing Values

Multi matrix analysis of multiple proteomics datasets on peptide level

Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

NanoString GeoMx Tools

NanoString nCounter Tools

neoantigen prediction from NGS sequencing data

Non-parametric analysis of response curves for thermal proteome profiling experiments

Normalization of Mass Spectrometry Data

ODE add-on to CellNOptR

Omics Data Integration Project

Omics Longitudinal Differential Analysis

Outlier Protein and Phosphosite Target Identifier

Overlay omics data onto SBGN pathway diagram

PAA (Protein Array Analyzer)

Package to Draw Protein Schematics from Uniprot API output

parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)

parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)

parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

Parsing pepXML files and filter based on peptide FDR.

PatchseqMap

PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

Peak Detection for Mass Spectrometry data using wavelet-based algorithms

Peptide Annotation and Data Visualization using Gviz

Peptide correlation analysis

Perform co-DE gene analysis

PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data

Phenotypes and cellular organizational units

Phenotypic EMD for comparison of single-cell samples

pIR: Estimating Isoelectric Point (pI) of Peptide and Proteins from Amino Acid Sequence.

PKG_TITLE

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Power Estimation Tool for RNA-Seq and proteomics data

Predict Acetylated Lysine Sites

Predicting Interactomes from Co-Elution

Prediction of Oligomerization of Coiled Coil Proteins

Prediction of pathway-related protein-protein interaction networks

Preprocessing of FIA-HRMS data

Probe-level Expression Change Averaging

Profiling and Analyzing Intrinsically Disordered Proteins in R

Protease Mapping

Protein annotation data package builder

Protein co-expression network analysis (ProCoNA).

Protein Micro Array Data Management and Interactive Visualization

Protein Profiling

Protein-Protein Interaction Statistical Package

Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Proteomics Label Free Quantification

protrusionproteome

Provides a GUI for DAPAR

Provides a GUI for rTANDEM

Quality Control of Protemics Data

Quantitative features for mass spectrometry data

Rank Product method for identifying differentially expressed genes with application in meta-analysis

R/Bioconductor tools for mass spectrometry-based proteomics

Regression Models with Multivariate Outcomes for Mass Cytometry Experiments

Reproducibility-Optimized Test Statistic

Retrieve and analyze data from the Human Protein Atlas

Rhythmicity Analysis Incorporating Non-parametric Methods

RIC (RNA interaction capture)

R interface to a subset of OpenBabel functionalities

R interface to PSI-MI 2.5 files

R interface to the pepXML standard

R Interface to the ProteomeXchange Repository

R Interface with InterMine-Powered Databases

Robust differential co-expression test by copula

Robust statistical inference for quantitative LC-MS proteomics

S4 generic functions for Bioconductor proteomics infrastructure

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

Shiny-based interactive data-quality exploration for omics data

Signature-based Clustering for Diagnostic Purposes

Signature discovery from omics data

Similarity measures for chemical compounds

Simulation of MSnSet Objects

Simulation tool for optimal design of high-dimensional MS-based proteomics experiment

Spatial Overlay for Omic Data from Nanostring GeoMx Data

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Spectra Infrastructure for Mass Spectrometry Data

Spectrum Infrastructure for Mass Spectrometry Data

SQL-based Mass Spectrometry Data Backend

Statistical analysis of hydrogen deuterium exchange mass spectrometry

Statistical Analysis of Molecular Profiles

Statistical Characterization of Post-translational Modifications

Statistical Modelling of AP-MS Data (SMAD)

Statistical Tools for volume data from 2D Gel Electrophoresis

Stoichiometry analysis of label-free proteomics data

SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome

Synthetic Lethal Genetic Interaction

System-wise protein turnover curve fitting

The PepBedR is an R-package to analyze peptide based Bed and bigBed files.

Thermal proximity co-aggregation with R

Time-Course Multi-Omics data integration

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Tools for qPLEX-RIME data analysis

Tools for quantitative proteomics data analysis

Tools for the Differential Analysis of Proteins Abundance with R

tool to run PHONEMeS on phosphoproteomic data

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Transform and Filter SWATH Data for Statistical Packages

Transform public proteomics data resources into Bioconductor Data Structures

Turn Bioconductor objects into tidy data frames

Unified statistal Modeling of Omics Data

User-friendly Workflow for Pre-processing and Statistical Analysis of Mass Spectrometry Data

Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression

Using Mass Cytometry for Differential Abundance Analyses

Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Visualising and Exploring Spectra Data

Visualization and management of the protein-protein interaction networks.

Well Plate Maker

What the package does (short line)

Biocview "Proteomics"

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