Genomic Data Retrieval with R

• UpdatedFeb 3, 2025
• R

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities

• UpdatedMar 12, 2025
• C#

Genome wide orthology inference and dNdS estimation

• UpdatedOct 10, 2023
• R

Matrix dissimilarity from the differences of Moments and sparsity

• UpdatedFeb 9, 2024
• R

Tools for Batch Effects Diagnostics and Correction

• UpdatedApr 1, 2023
• R

Construction, quantification, and visualization of proteoform families

• UpdatedDec 16, 2024
• C#

An alignment-independent tool for the study of pathogen sequence diversity

• UpdatedApr 30, 2023
• Python

Workflow for prOteome and tRanScriptome functiOnal aNnotation. CAUTION : project has moved to Gitlab.

• UpdatedMar 3, 2023
• Nextflow

Supplementary data and pipelines for analyzing genome gene content data and morphology to create various phylogenies.

• UpdatedMay 4, 2023
• R

Scripts used for the phosho data analysis

• UpdatedMar 31, 2022
• Jupyter Notebook

Sharing some useful biological data that I generated during my PhD.

• UpdatedMar 4, 2022

Hydrophobicity of the human proteome

• UpdatedMar 11, 2024
• HTML

Proteome Discoverer Result File Reader

• UpdatedDec 4, 2024
• Jupyter Notebook

This repository contains a set of scripts and workflows designed to search for Respiratory Complex I (NADH Ubiquinone Oxidoreductase) subunits in prokaryotic genomes and proteomes.

• UpdatedMar 10, 2025
• Jupyter Notebook

Blast wrapper using snakemake to generate correspondance between a list of transcript or protein and some proteomes.

• UpdatedSep 6, 2022
• Python

• UpdatedAug 25, 2020
• Python

It assigns the phosphorylation site in protein

• UpdatedAug 4, 2022
• R

CWL descriptions for FragPipe Proteomics Pipline

• UpdatedApr 5, 2022
• Common Workflow Language

This is now the main repository. A few older issues are still tracked on gitlab for reference.

• UpdatedSep 6, 2023
• Jupyter Notebook

This repository is to store the used dataset for publications related to UNIQmin

• UpdatedJul 28, 2023