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
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
Accelerated similarity searching of small molecules
A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.
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 Framework for Quality Control
A Framework for Quality Control
A Framework for Quality Control
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
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 and quantitation of isobarically tagged MSMS proteomics data
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 interface between R and MS-GF+
An mzIdentML parser for R
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 R package for proteomics data quality control
An R package for proteomics data quality control
An R package for proteomics data quality control
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
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 the clinical proteomic profiling data analysis
A package for variant peptides detection and visualization in shotgun proteomics.
A package for variant peptides detection and visualization in shotgun proteomics.
A shiny GUI for MSGFplus
A shiny GUI for MSGFplus
A shiny GUI for MSGFplus
A shiny GUI for MSGFplus
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 unifying bioinformatics framework for spatial proteomics
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 Functions and Classes for Mass Spectrometry and Proteomics
Bioc2014 workshop on R / Bioconductor packages for Proteomics
BraDiPluS - Braille Display Plugs Data Analysis
Causal network analysis methods
Causal network analysis methods
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Ciphergen SELDI-TOF Processing
Ciphergen SELDI-TOF Processing
Cleavage of Polypeptide Sequences
Cleavage of Polypeptide Sequences
Cleavage of Polypeptide Sequences
Compensates for the bias introduced by median normalization in phosphoproteomics
Compensates for the bias introduced by median normalization in phosphoproteomics
Conversion between the Workflow4metabolomics tabulated format and the ExpressionSet bioconductor class
Cross-target analysis of small molecule bioactivity
Cross-target analysis of small molecule bioactivity
Cross-target analysis of small molecule bioactivity
Cross-target analysis of small molecule bioactivity
deltaGseg
deltaGseg
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Differential Enrichment analysis of Proteomics data
Encapsulate X!Tandem in R.
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Exploratory Data Analysis of LC-MS/MS data by spectral counts
Exploratory Data Analysis of LC-MS/MS data by spectral counts
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
f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics
Functionality to Read and Manipulate SomaLogic ADAT files
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 database from NGS data, with a focus on RNA-Seq data, for proteomics search
Generating SAM file for PSMs in shotgun proteomics data
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
High throughput prioritized acquisition and processing of tandem mass spectra
Human Protein Atlas in R
Human Protein Atlas in R
Human Protein Atlas in R
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 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, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
In Silico Interactome
In Silico Interactome
Integration of CellNOptR to add missing links
Integration of CellNOptR to add missing links
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
Interfaces the tandem protein identification algorithm in R
Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching
Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching
Label-free data analysis pipeline for optimal identification and quantitation
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
LC-MS/MS Differential Expression Tests
Local Pooled Error Test for Differential Expression with Paired High-throughput Data
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
Manipulating and exploring protein and proteomics data
Manipulating and exploring protein and proteomics data
Mass spectrum processing by wavelet-based algorithms
Mass spectrum processing by wavelet-based algorithms
Mismatch Tolerant Maximum Common Substructure Searching
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
neoantigen prediction from NGS sequencing data
neoantigen prediction from NGS sequencing data
ODE add-on to CellNOptR
ODE add-on to CellNOptR
PAA (Protein Array Analyzer)
PAA (Protein Array Analyzer)
parser for netCDF, mzXML, mzData 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 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.
Parsing pepXML files and filter based on peptide FDR.
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
Peptide Annotation and Data Visualization using Gviz
Peptide Annotation and Data Visualization using Gviz
Peptide Annotation and Data Visualization using Gviz
PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data
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
Phenotypes and cellular organizational units
pIR: Estimating Isoelectric Point (pI) of Peptide and Proteins from Amino Acid Sequence.
Predict Acetylated Lysine Sites
Predict Acetylated Lysine Sites
Prediction of Oligomerization of Coiled Coil Proteins
Prediction of Oligomerization of Coiled Coil Proteins
Prediction of pathway-related protein-protein interaction networks
Prediction of pathway-related protein-protein interaction networks
Preprocessing of FIA-HRMS data
Preprocessing of FIA-HRMS data
Probe-level Expression Change Averaging
Probe-level Expression Change Averaging
Protein annotation data package builder
Protein annotation data package builder
Protein co-expression network analysis (ProCoNA).
Protein co-expression network analysis (ProCoNA).
Protein co-expression network analysis (ProCoNA).
Protein Profiling
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
Provides a GUI for DAPAR
Provides a GUI for DAPAR
Provides a GUI for DAPAR
Provides a GUI for rTANDEM
Provides a GUI for rTANDEM
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Rank Product method for identifying differentially expressed genes with application in meta-analysis
R/Bioconductor tools for mass spectrometry-based proteomics
Reproducibility-Optimized Test Statistic
Reproducibility-Optimized Test Statistic
Rhythmicity Analysis Incorporating Non-parametric Methods
Rhythmicity Analysis Incorporating Non-parametric Methods
R interface to a subset of OpenBabel functionalities
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 to the ProteomeXchange Repository
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
S4 generic functions for Bioconductor proteomics infrastructure
S4 generic functions for Bioconductor proteomics infrastructure
S4 generic functions for Bioconductor proteomics infrastructure
Signature discovery from omics data
Signature discovery from omics data
Similarity measures for chemical compounds
Similarity measures for chemical compounds
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Statistical Tools for volume data from 2D Gel Electrophoresis
Statistical Tools for volume data from 2D Gel Electrophoresis
Synthetic Lethal Genetic Interaction
Synthetic Lethal Genetic Interaction
Tools for the Differential Analysis of Proteins Abundance with R
Tools for the Differential Analysis of Proteins Abundance with R
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
Transform public proteomics data resources into Bioconductor Data Structures
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Using Mass Cytometry for Differential Abundance Analyses
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
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Visualization and management of the protein-protein interaction networks.
Visualization and management of the protein-protein interaction networks.