Scientific Tools
1. MSigDF Package
MSigDF: Molecular Signatures Database in Tidy Format
A up to date fork of the Molecular Signatures Database (MSigDB) into a tibble format originally created by Stephen Turner, this updated version is up to date with MSigDB 2025.1 .
Applications: Gene set enrichment analysis - Pathway analysis - Functional genomics research - Bioinformatics workflows
Tech Stack: R, tidyverse, bioinformatics, tidy-data, msigdb
2. PubMatrixR Package
PubMatrixR: Systematic Literature Search
(PubMatrixR) is an R package that performs systematic literature searches on PubMed and PMC databases using pairwise combinations of search terms. It creates co-occurrence matrices showing the number of publications that mention both terms from two different sets, enabling researchers to explore relationships between genes, diseases, pathways.
Applications: Biomedical Data Exploration
Based on paper : PubMatrix: a tool for multiplex literature mining of Becker KG et al. BMC Bioinformatics. 2003 Dec 10;4:61. doi: 10.1186/1471-2105-4-61
First forked from: https://github.com/tslaird/PubMatrixR
3. Blind Rename Files
Blind Rename Files Swift macOS App & Bash Scripts
Rename files on folder for manual image blind analysis to avoid bias.
A swift OSX app or a bash-script to rename file, thinking in avoiding bias in manual image quantification. From the times I was doing this with ImageJ/Fiji.
Applications: Semi-automatic/manual image quantification.