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Search results for r proteomics

51 search results found

Teachingmaterial ⭐ 161

Various teaching material

Msnbase ⭐ 115

Base Classes and Functions for Mass Spectrometry and Proteomics

Rforproteomics ⭐ 69

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

Olinkrpackage ⭐ 68

Olink R package: A collection of functions to facilitate analysis of proteomic data from Olink. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.

Picotti lab data analysis package.

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

R package for analysing proteomics data

Compare different differential abundance and expression methods

Brings Orbitrap Mass Spectrometry Data to Life; Multi-platform, Fast and Colorful R package.

Low level infrastructure to handle MS spectra

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)

Somadataio ⭐ 20

The SomaDataIO package loads and exports 'SomaScan' data via the 'SomaLogic Operating Co., Inc.' proprietary data file, called an ADAT ('*.adat'). The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.

Qfeatures ⭐ 19

Quantitative features for mass spectrometry data

Single cell proteomics data processing

Proteomics Toolset for Integrative Data Analysis

amica: an interactive and user-friendly web-based platform for the analysis of proteomics data

Mscoreutils ⭐ 16

Core Utils for Mass Spectrometry Data

Rformassspectrometry ⭐ 15

The R for Mass Spectrometry meta-package

CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Normalyzerde ⭐ 14

Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.

Analytical R Tools for Mass Spectrometry

feseR: Combining feature selection methods for analyzing omics data

A unifying bioinformatics framework for organelle proteomics

Pomashiny ⭐ 11

🍎 Web-based User-friendly Workflow for Metabolomics and Proteomics Data Analysis

Cell-type Relationship Analysis Workflow Done Across Distances

Msimpute ⭐ 10

Methods for label-free mass spectrometry proteomics

Secretsanta ⭐ 9

flexible pipelines for scalable secretome prediction, R package

isobar - R library for the Analysis and quantitation of isobarically tagged MSMS proteomics data

Irs_normalization ⭐ 9

An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

A comprehensive R package for label-free proteomics data analysis and modeling

Lgatto.github.io ⭐ 8

Nonparametric Analysis of Response Curves from Thermal Proteome Profiling Experiments

An R package of High-resolution Informatics Toolbox for Maldi-imaging Proteomics

Amp_phase1_ra ⭐ 8

🌾 Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.

Tmt_analysis_examples ⭐ 7

Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.

Msquality ⭐ 6

Msstatsconvert ⭐ 6

Converter functions for the MSstats package

Avant_garde ⭐ 6

Avant-garde (AvG) is a new tool to refine Data-Independent Acquisition (and Parallel Reaction Monitoring) by removing interfered transitions, adjusting integration boundaries and scoring peaks to control the FDR.

Msstatsptm ⭐ 6

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Provision ⭐ 6

Shiny app for proteomics data analysis

R package for easy interop between Perseus and R

Prolocgui ⭐ 6

Interactive visualisation and exploration of spatial proteomics data

Motrpacbicqc ⭐ 6

R package for the MoTrPAC community

Matrixqcvis ⭐ 5

custom wrappers of frequently used R code

Amino acid modifications for mass spectrometry

Protgenerics ⭐ 5

S4 generic functions for Bioconductor mass spectrometry infrastructure

Differential expression analysis for mass spectrometry proteomics and metabolomics

Kinase Activity Predictions from shotgun proteomics

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