Biocview "Proteomics"

A bioconductor package for exploration of alignment gap positions from RNA-seq data
A bioconductor package for exploration of alignment gap positions from RNA-seq data
Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
A collection of tools for imaging MS data processing
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
Add-on to CellNOptR: Discretized time treatments
A DownStream Chemo-Proteomics Analysis Pipeline
A DownStream Chemo-Proteomics Analysis Pipeline
A DownStream Chemo-Proteomics Analysis Pipeline
A Framework for Quality Control
A Framework for Quality Control
A graphical user interface for MSstatsQC package
A graphical user interface for MSstatsQC package
A k-tables approach to integrate multiple Omics-Data
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 and quantitation of isobarically tagged MSMS proteomics data
Analysis of pulsed-SILAC quantitative proteomics data
Analysis of pulsed-SILAC quantitative proteomics data
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analyze thermal proteome profiling (TPP) experiments
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 interface between R and MS-GF+
An interface between R and MS-GF+
An mzIdentML parser for R
An mzIdentML parser for R
An package for identification of novel peptides by customized database derived from RNA-Seq
An package for identification of novel peptides by customized database derived from RNA-Seq
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 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
A shiny GUI for MSGFplus
A shiny GUI for MSGFplus
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
Assess Gene Predictions Using Proteomics and Evolutionary Conservation
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 set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions
Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions
A unifying bioinformatics framework for spatial proteomics
A unifying bioinformatics framework for spatial proteomics
Baffling Recursive Algorithm for Isotope distributioN calculations
Baffling Recursive Algorithm for Isotope distributioN calculations
Base Functions and Classes for Mass Spectrometry and Proteomics
Base Functions and Classes for Mass Spectrometry and Proteomics
Base NanoString Experiment Class
Bioc2014 workshop on R / Bioconductor packages for Proteomics
Biological Network Analysis
Biological Network Analysis
BraDiPluS - Braille Display Plugs Data Analysis
Causal network analysis methods
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Ciphergen SELDI-TOF Processing
Cleavage of Polypeptide Sequences
Cleavage of Polypeptide Sequences
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
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
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
Core Utils for Mass Spectrometry Data
COSMOS (Causal Oriented Search of Multi-Omic Space)
COSMOS (Causal Oriented Search of Multi-Omic Space)
Covariate Assisted Large-scale Multiple testing
Covariate Assisted Large-scale Multiple testing
Cross-target analysis of small molecule bioactivity
Cross-target analysis of small molecule bioactivity
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
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)
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 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 discovery in high-dimensional cytometry via high-resolution clustering
Differential Enrichment analysis of Proteomics data
Differential Enrichment analysis of Proteomics data
Differential Enrichment analysis of Proteomics data
Differential expression using kernel-based score test
Diffusion scores on biological networks
Diffusion scores on biological networks
Diffusion scores on biological networks
Direct Access to Orbitrap Data and Beyond
Direct Access to Orbitrap Data and Beyond
Downstream analysis of the MaxQuant output
Drug-Target Interactions
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Effective mobility scale transformation of CE-MS(/MS) data
Effective mobility scale transformation of CE-MS(/MS) data
Effective mobility scale transformation of CE-MS(/MS) data
Encapsulate X!Tandem in R.
Ensemble of Gene Set Enrichment Analyses
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
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
Exposome and omic data associatin and integration analysis
Expression Weighted Celltype Enrichment
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
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
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
Generic infrastructure for Bioconductor mass spectrometry packages
Genetic inteRaction and EssenTiality neTwork mApper
Handling and Managing Peptide Spectrum Matches
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
Human Protein Atlas in R
Identification and Annotation of Protein Hotspot Residues
Identification and Annotation of Protein Hotspot Residues
Identification of Mutational Clusters in 3D Protein Space via Simulation.
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 Mutational Clusters in Proteins via a Graph Theoretical Approach.
Identification of Protein Amino acid Clustering
Identification of Protein Amino acid Clustering
Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
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
Imputation of label-free mass spectrometry peptides
Infrastructure for chromatographic representation of 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
Integration of CellNOptR to add missing links
Integration of CellNOptR to add missing links
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Interactive visualisation of spatial proteomics data
Interactive visualisation of spatial proteomics data
Interactive visualisation of spatial proteomics data
Interfaces the tandem protein identification algorithm in R
Interlog protein network reconstruction by Mapping and Mining ANalysis
Interlog protein network reconstruction by Mapping and Mining ANalysis
Investigation of Fragmentation Conditions in Top-Down Proteomics
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
KinSwingR: network-based kinase activity prediction
Label-free data analysis pipeline for optimal identification and quantitation
Label-free data analysis pipeline for optimal identification and quantitation
LC-MS/MS Differential Expression Tests
Linear Models for Microarray Data
Linear Models for Microarray Data
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
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
Longitudinal system suitability monitoring and quality control for proteomic experiments
Managing amino acid modifications for mass spectrometry
Manipulating and exploring protein and proteomics data
Manipulating and exploring protein and proteomics data
Marker Enrichment Modeling (MEM)
Marker Enrichment Modeling (MEM)
MassQL support for Spectra
Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
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 Mascot Generic Format (mgf) Files
Mass Spectrometry Data Backend for NIST msp Files
Mass Spectrometry Data Backend for NIST msp Files
Mass spectrometry data backends for The Human Metabolome Database
Mass spectrometry data backends for The Human Metabolome Database
Mass spectrum processing by wavelet-based algorithms
Mean/Median-balanced quantile normalization
Mean/Median-balanced quantile normalization
Mean/Median-balanced quantile normalization
Minimal Protein Set Explaining Peptide Spectrum Matches
Minimal Protein Set Explaining Peptide Spectrum Matches
Miscellaneous functions used by Vlad Petyuk for proteomics data analysis
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
MsQuality - Quality metric calculation from Spectra and MsExperiment objects
MsQuality - Quality metric calculation from Spectra and MsExperiment objects
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
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
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
NanoString GeoMx Tools
NanoString nCounter Tools
neoantigen prediction from NGS sequencing data
neoantigen prediction from NGS sequencing data
Non-parametric analysis of response curves for thermal proteome profiling experiments
Non-parametric analysis of response curves for thermal proteome profiling experiments
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 Data Integration Project
Omics Data Integration Project
Omics Longitudinal Differential Analysis
Omics Longitudinal Differential Analysis
Outlier Protein and Phosphosite Target Identifier
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
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
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 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
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
Phenotypic EMD for comparison of single-cell samples
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
Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
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
Power Estimation Tool for RNA-Seq and proteomics data
Predict Acetylated Lysine Sites
Predicting Interactomes from Co-Elution
Predicting Interactomes from Co-Elution
Predicting Interactomes from Co-Elution
Prediction of Oligomerization of Coiled Coil Proteins
Prediction of Oligomerization of Coiled Coil Proteins
Prediction of pathway-related protein-protein interaction networks
Preprocessing of FIA-HRMS data
Preprocessing of FIA-HRMS data
Probe-level Expression Change Averaging
Profiling and Analyzing Intrinsically Disordered Proteins in R
Profiling and Analyzing Intrinsically Disordered Proteins in R
Protease Mapping
Protein annotation data package builder
Protein co-expression network analysis (ProCoNA).
Protein co-expression network analysis (ProCoNA).
Protein Micro Array Data Management and Interactive Visualization
Protein Profiling
Protein-Protein Interaction Statistical Package
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 DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
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
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
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 DAPAR
Provides a GUI for DAPAR
Provides a GUI for DAPAR
Provides a GUI for rTANDEM
Quality Control of Protemics Data
Quality Control of Protemics Data
Quality Control of Protemics Data
Quality Control of Protemics Data
Quantitative features for mass spectrometry data
Quantitative features for mass spectrometry data
Quantitative features for mass spectrometry 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
Retrieve and analyze data from the Human Protein Atlas
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 a subset of OpenBabel functionalities
R interface to PSI-MI 2.5 files
R interface to PSI-MI 2.5 files
R interface to PSI-MI 2.5 files
R interface to the pepXML standard
R interface to the pepXML standard
R Interface to the ProteomeXchange Repository
R Interface to the ProteomeXchange Repository
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
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"
"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-based Clustering for Diagnostic Purposes
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
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
Spectra Infrastructure for Mass Spectrometry Data
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 Analysis of Molecular Profiles
Statistical Characterization of Post-translational Modifications
Statistical Characterization of Post-translational Modifications
Statistical Characterization of Post-translational Modifications
Statistical Characterization of Post-translational Modifications
Statistical Modelling of AP-MS Data (SMAD)
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
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
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.
The PepBedR is an R-package to analyze peptide based Bed and bigBed files.
Thermal proximity co-aggregation with R
Thermal proximity co-aggregation with R
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
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
Tools for the Differential Analysis of Proteins Abundance with R
Tools for the Differential Analysis of Proteins Abundance with R
Tools for the Differential Analysis of Proteins Abundance with R
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
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation 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 and Filter SWATH Data for Statistical Packages
Transform public proteomics data resources into Bioconductor Data Structures
Transform public proteomics data resources into Bioconductor Data Structures
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Unified Statistal Modeling of Omics Data
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 Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Using Mass Cytometry for Differential Abundance Analyses
Using Mass Cytometry for Differential Abundance Analyses
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
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
Well Plate Maker
What the package does (short line)