Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
☆101Aug 20, 2025Updated 6 months ago
Alternatives and similar repositories for RforProteomics
Users that are interested in RforProteomics are comparing it to the libraries listed below
Sorting:
- ☆17Sep 28, 2022Updated 3 years ago
- Base Classes and Functions for Mass Spectrometry and Proteomics☆136Aug 26, 2025Updated 6 months ago
- A unifying bioinformatics framework for organelle proteomics☆16Nov 5, 2025Updated 4 months ago
- Differential Expression Analysis tool box R lang package for omics data☆47Feb 25, 2026Updated last week
- Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics☆128Jan 13, 2026Updated last month
- PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering☆125Feb 12, 2026Updated 3 weeks ago
- DEqMS is a tool for quantitative proteomic analysis☆24Apr 16, 2025Updated 10 months ago
- R-Shiny GUI integrated with the MSstats package family☆20Updated this week
- TIMEOR: Trajectory Inference and Mechanism Exploration with Omics Data in R☆17Feb 22, 2022Updated 4 years ago
- R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass …☆30Jul 28, 2025Updated 7 months ago
- ☆69May 7, 2024Updated last year
- Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆16Dec 8, 2021Updated 4 years ago
- pathfindR: Enrichment Analysis Utilizing Active Subnetworks☆196Dec 22, 2025Updated 2 months ago
- Nonparametric Analysis of Response Curves from Thermal Proteome Profiling Experiments☆13May 8, 2023Updated 2 years ago
- ☆16Jul 18, 2022Updated 3 years ago
- a deep generative model for single-cell survival analysis☆16Dec 2, 2025Updated 3 months ago
- Protocol of the analysis of iTRAQ/TMT proteomics data including quantification, statistical analysis and maybe clustering☆12May 4, 2019Updated 6 years ago
- Analysis of cell-cell communication at single-cell resolution☆106Sep 10, 2024Updated last year
- BANDITS: Bayesian ANalysis of DIfferenTial Splicing☆19Sep 29, 2025Updated 5 months ago
- Single cell proteomics data processing☆30Feb 9, 2026Updated last month
- This is a collection of minimal code to visualize various aspects of proteomics data.☆82Jan 6, 2022Updated 4 years ago
- R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.☆17Updated this week
- DIA-NN - a universal automated software suite for DIA proteomics data analysis.☆427Feb 5, 2026Updated last month
- Open source Java library for computational proteomics☆34Feb 25, 2026Updated last week
- ☆57Jan 2, 2024Updated 2 years ago
- Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.☆26Mar 3, 2026Updated last week
- Semi-supervised learning for peptide identification from shotgun proteomics datasets☆144Nov 21, 2025Updated 3 months ago
- Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data☆31Oct 5, 2022Updated 3 years ago
- A tool integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.☆13Updated this week
- Workflow for ZINB-WaVE + DESeq2 intergration for single-cell RNA-seq☆30Jan 6, 2021Updated 5 years ago
- A collection of available Python tools for Proteomics analysis☆66Jan 31, 2026Updated last month
- Deep learning-based pseudo mass spectrometry imaging☆14Jul 2, 2022Updated 3 years ago
- R functions underlying OmicsNet☆20Feb 10, 2026Updated last month
- The R for Mass Spectrometry meta-package☆18Dec 24, 2023Updated 2 years ago
- Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono☆239Feb 26, 2026Updated last week
- An S3 data object and framework for common quantitative proteomic analyses☆47Dec 15, 2025Updated 2 months ago
- All data and notebook for my 2020 scRNA-seq analysis workshop☆18Jul 27, 2020Updated 5 years ago
- Tools for Batch Effects Diagnostics and Correction☆17Apr 25, 2025Updated 10 months ago
- Documentation is available here:☆24Dec 9, 2025Updated 3 months ago